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return the principle root. | return the principal root. | def nth_root(self, n): """ Return the nth root of this number. | 4bdf08a997ab55d67dd48b374fa3d4cbb7ddbd56 /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/9890/4bdf08a997ab55d67dd48b374fa3d4cbb7ddbd56/qqbar.py | [
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self.assertEqual(u.fp.fp.raw._sock.gettimeout(), 120) | self.assertEqual(u.fp.raw._sock.gettimeout(), 120) | def test_http_timeout(self): u = _urlopen_with_retry("http://www.python.org", timeout=120) self.assertEqual(u.fp.fp.raw._sock.gettimeout(), 120) | 5ce8975a83a5664bc531c881eb9c98ebf09801e3 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/8125/5ce8975a83a5664bc531c881eb9c98ebf09801e3/test_urllib2net.py | [
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def getHash(self): return len(DebugClass.itemlist) | assert self.dprint(items) for i in range(len(items)): self.Check(i, self.isChecked(i)) self.Bind(wx.EVT_CHECKLISTBOX, self.OnCheckListBox) | def getHash(self): return len(DebugClass.itemlist) | 56ac591d312ea693f3992735f261bc9a7c0cde45 /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/11522/56ac591d312ea693f3992735f261bc9a7c0cde45/debug_classes.py | [
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parent = wx.GetApp().mainFrame | app = wx.GetApp() if app is not None: parent = app.mainFrame | def get(view, parent=None, testPassword=None): """ Get the master password. If needed, it will be asked from the user. Safe to call from from a background thread. @raise NoMasterPassword: NoMasterPassword will be raised if we have a non-default master password that has timed out, and the user cancels the dialog where we ask for it. @param view: Repository view. @return: deferred """ if _timer is not None: _timer.cancel() prefs = schema.ns("osaf.framework.MasterPassword", view).masterPasswordPrefs if not prefs.masterPassword: return '' # Return the cached password if we have it if _masterPassword is not None: # Reset timer _setTimedPassword(_masterPassword, prefs.timeout * 60) return _masterPassword # Otherwise, let's ask the user... from osaf.framework import password if testPassword is not None: passwords = [testPassword] else: passwords = [item for item in password.Password.iterItems(view)] if parent is None: parent = wx.GetApp().mainFrame while True: dlg = GetMasterPasswordDialog(parent, prefs.timeout) if wx.Platform == '__WXMAC__': dlg.CenterOnParent() try: if dlg.ShowModal() != wx.ID_OK: raise password.NoMasterPassword(_(u'No master password')) pword, timeout = dlg.getPasswordAndTimeout() finally: dlg.Destroy() again = False for item in passwords: if not waitForDeferred(item.initialized()): continue try: waitForDeferred(item.decryptPassword(masterPassword=pword)) break except password.DecryptionError: again = True break else: raise RuntimeError('At least one password was expected to be initialized') if again: wx.MessageBox (_(u'Master password was incorrect, please try again.'), _(u'Incorrect password'), parent=parent) continue break if prefs.timeout != timeout: prefs.timeout = timeout view.commit() _setTimedPassword(pword, timeout * 60) return _masterPassword | 51897aa3f2b00065302646e2e9094f4d63a8782b /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/9228/51897aa3f2b00065302646e2e9094f4d63a8782b/MasterPassword.py | [
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class StrokeOrderBuilder(CSVFileLoader): | class NarrowBuildCSVFileLoader(CSVFileLoader): """ A CSVFileLoader that ignores entries for Unicode characters outside the BMP. """ @classmethod def getDefaultOptions(cls): options = super(NarrowBuildCSVFileLoader, cls).getDefaultOptions() options.update({'wideBuild': True}) return options @classmethod def getOptionMetaData(cls, option): optionsMetaData = {'wideBuild': {'type': 'bool', 'description': "include characters outside the Unicode BMP"}} if option in optionsMetaData: return optionsMetaData[option] else: return super(NarrowBuildCSVFileLoader, cls).getOptionMetaData( option) def filterEntry(self, entryDict): if (entryDict and 'ChineseCharacter' in entryDict and entryDict['ChineseCharacter'] > u'\U00010000'): return None return entryDict class StrokeOrderBuilder(NarrowBuildCSVFileLoader): | def build(self): import codecs | ec20f0cb3b7d6f3d33d81ca502fd1939f9d56e73 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/11128/ec20f0cb3b7d6f3d33d81ca502fd1939f9d56e73/builder.py | [
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return super(osv.osv,self).write(cr, uid, ids, vals, context) | return super(task,self).write(cr, uid, ids, vals, context) | def write(self, cr, uid, ids,vals,context={}): if (vals.has_key('project_id') and vals['project_id']) or (vals.has_key('name') and vals['name']): vals_line = {} hr_anlytic_timesheet = self.pool.get('hr.analytic.timesheet') task_obj_l = self.browse(cr, uid, ids, context) if (vals.has_key('project_id') and vals['project_id']): project_obj = self.pool.get('project.project').browse(cr, uid, vals['project_id']) acc_id = project_obj.category_id.id | a9f6551f879763c23ece121459a21f76bb874ebf /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/7397/a9f6551f879763c23ece121459a21f76bb874ebf/project_timesheet.py | [
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self.unpack_tarball( tarball_path ) | self.unpack_tarball( tarball_path, self.boost_root ) | def get_tarball( self, *args ): if not args or args == []: args = [ 'download', 'unpack' ] | 3f0366c1d4e33eca4693567235cd2cbe44e6bfde /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/7959/3f0366c1d4e33eca4693567235cd2cbe44e6bfde/regression.py | [
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_, stepless_data = zip(*data) | if min_step is not None: data = [(step, tup) for step, tup in data if min_step <= step] if max_step is not None: data = [(step, tup) for step, tup in data if step <= max_step] stepless_data = [tup for step, tup in data] | def get_plot_data(self, expr_x, expr_y): """Generate plot-ready data. | e95d25887b561966f6c5076fe18c3901d1d73897 /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/12871/e95d25887b561966f6c5076fe18c3901d1d73897/log.py | [
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pass | def __init__(self, script_args=None, exit_code=None, message=None, output=None, cwd=None): if not message: message = 'Failed to run "%s"' % script_args if exit_code: message += " exit_code: %d" % exit_code if cwd: message += " cwd: %s" % cwd Exception.__init__(self, message) self.script_args = script_args self.exit_code = exit_code self.output = output self.cwd = cwd def message_with_output(self, output_limit=500): if self.output: if len(self.output) > output_limit: return "%s\nLast %s characters of output:\n%s" % (self, output_limit, self.output[-output_limit:]) return "%s\n%s" % (self, self.output) return str(self) | def message(self): return "\n".join(self.message_lines) + "\n" | cbfef173775a18c163a046efa120abeeff3a6751 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/9392/cbfef173775a18c163a046efa120abeeff3a6751/scm.py | [
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for dn in ticket_dn_list: | print job_dn_list for dn,group in ticket_dn_list: print dn,group | def execute(self): """ The main agent execution method """ | 1cff06ebf279b10e12a27c88249cd250a48ec3fb /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/12864/1cff06ebf279b10e12a27c88249cd250a48ec3fb/ProxyRenewalAgent.py | [
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bosh.dirs['Fraps'], Image(r'images/fraps.png'), _("Launch Fraps"))) | bosh.dirs['Fraps'], Image(r'images/fraps.png'), _("Launch Fraps"))) | def InitStatusBar(): """Initialize status bar links.""" #--Bash Status/LinkBar #BashStatusBar.buttons.append(App_Fallout3()) BashStatusBar.buttons.append(Fose_Button()) BashStatusBar.buttons.append(AutoQuit_Button()) BashStatusBar.buttons.append( Fallout3_Button( bosh.dirs['app'].join('Fallout3.exe'), Image(r'images/fallout3.png'), _("Launch Fallout3"), _("Launch Fallout3 + FOSE"), '')) BashStatusBar.buttons.append( App_Button( bosh.dirs['app'].join('GECK.exe'), Image(r'images/geck.png'), _("Launch GECK"), _("Launch GECK + FOSE"), '-editor')) BashStatusBar.buttons.append( App_Button( bosh.dirs['app'].join('fomm\\fomm.exe'), Image(r'images/database_connect.png'), _("Launch FOMM"))) BashStatusBar.buttons.append( App_FO3Edit( (bosh.dirs['FO3EditPath'], '-view'), Image(r'images/brick_edit.png'), _("Launch FO3View"))) BashStatusBar.buttons.append( App_FO3Edit( dirs['FO3EditPath']), Image(r'images/brick.png'), _("Launch FO3Edit"))) BashStatusBar.buttons.append( App_FO3Edit( (dirs['FO3EditPath'],'-translate'), Image(r'images/brick_error.png'), _("Launch FO3Trans"))) BashStatusBar.buttons.append( App_BOSS( bosh.dirs['app'].join('Data\\BOSS-F.bat'), Image(r'images/Boss1.png'), _("Launch BOSS"))) BashStatusBar.buttons.append( App_BOSS( bosh.dirs['app'].join('Data\\BOSS-F.bat'), Image(r'images/boss2.png'), _("Launch BOSS"))) if bosh.inisettings['showmodelingtoollaunchers']: BashStatusBar.buttons.append( App_Button( bosh.dirs['BlenderPath'], Image(r'images/blender.png'), _("Launch Blender"))) BashStatusBar.buttons.append( App_Button( bosh.dirs['GmaxPath'], Image(r'images/gmax.png'), _("Launch Gmax"))) BashStatusBar.buttons.append( App_Button( bosh.dirs['MayaPath'], Image(r'images/maya.png'), _("Launch Maya"))) BashStatusBar.buttons.append( App_Button( bosh.dirs['MaxPath'], Image(r'images/max.png'), _("Launch 3dsMax"))) if bosh.inisettings['showmodelingtoollaunchers'] or bosh.inisettings['showtexturetoollaunchers']: BashStatusBar.buttons.append( App_Button( bosh.dirs['NifskopePath'], Image(r'images/nifskope.png'), _("Launch Nifskope"))) if bosh.inisettings['showtexturetoollaunchers']: BashStatusBar.buttons.append( App_Button( bosh.dirs['GIMP'], Image(r'images/gimp.png'), _("Launch GIMP"))) BashStatusBar.buttons.append( App_Button( bosh.dirs['Photoshop'], Image(r'images/photoshop.png'), _("Launch Photoshop"))) BashStatusBar.buttons.append( App_Button( bosh.dirs['Artweaver'], Image(r'images/artweaver.png'), _("Launch Artweaver"))) BashStatusBar.buttons.append( App_Button( bosh.dirs['PaintNET'], Image(r'images/paint.net.png'), _("Launch Paint.NET"))) BashStatusBar.buttons.append( App_Button( bosh.dirs['DDSConverter'], Image(r'images/ddsconverter.png'), _("Launch DDSConverter"))) if bosh.inisettings['showaudiotoollaunchers']: BashStatusBar.buttons.append( App_Button( bosh.dirs['Audacity'], Image(r'images/audacity.png'), _("Launch Audacity"))) BashStatusBar.buttons.append( App_Button( bosh.dirs['Fraps'], Image(r'images/fraps.png'), _("Launch Fraps"))) BashStatusBar.buttons.append( App_Button( bosh.dirs['NPP'], Image(r'images/notepad++.png'), _("Launch Notepad++"))) BashStatusBar.buttons.append( App_Button( bosh.dirs['Custom1'], Image(r'images/custom1.png'), _(bosh.inisettings['custom1txt']))) BashStatusBar.buttons.append( App_Button( bosh.dirs['Custom2'], Image(r'images/custom2.png'), _(bosh.inisettings['custom2txt']))) BashStatusBar.buttons.append( App_Button( bosh.dirs['Custom3'], Image(r'images/custom3.png'), _(bosh.inisettings['custom3txt']))) BashStatusBar.buttons.append( App_Button( bosh.dirs['Custom4'], Image(r'images/custom4.png'), _(bosh.inisettings['custom4txt']))) BashStatusBar.buttons.append(App_BashMon()) BashStatusBar.buttons.append(App_DocBrowser()) BashStatusBar.buttons.append(App_ModChecker()) BashStatusBar.buttons.append(App_Help()) | 3ac43907fa076fea1e8d682219e2b28fc7419f7b /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/6682/3ac43907fa076fea1e8d682219e2b28fc7419f7b/basher.py | [
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if isinstance(x, float): | if isinstance(x, float): | def __call__(self, x): """ EXAMPLES:: | b8d4e8980196922bad05dde8387e4a6f47ddf4b0 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/9417/b8d4e8980196922bad05dde8387e4a6f47ddf4b0/other.py | [
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modifyAlignCommonAxisActionText = "<u><b>Align To Common Axis</b></u><br>"\ "<p><img source=\"ui/actions/Tools/Build Tools/AlignToCommonAxis.png\"><br> "\ "Aligns one or more chunks to the axis of the first selected chunk."\ "You must select two or more chunks before using this feature."\ "</p>" | modifyAlignCommonAxisActionText =\ "<u><b>Align To Common Axis</b></u><br>"\ "<p>"\ "<img source=\"ui/actions/Tools/Build Tools/AlignToCommonAxis.png\"><br> "\ "Aligns one or more chunks to the axis of the first selected chunk. "\ "You must select two or more chunks before using this feature."\ "</p>" | def createWhatsThisTextForMainWindowWidgets(win): """ Adds the "What's This" help text to items found in the NE1 mainwindow toolbars and menus . @param win: NE1's mainwindow object. @type win: U{B{QMainWindow}<http://doc.trolltech.com/4/qmainwindow.html>} @note: Property Managers specify "What's This" text for their own widgets, usually in a method called add_whats_this_text(), not in this file. """ # # File Toolbar # # Open File fileOpenText = "<u><b>Open File</b></u> (Ctrl + O)<br> "\ "<p><img source=\"ui/actions/File/Open.png\"><br> "\ "Opens a new file."\ "</p>" win.fileOpenAction.setWhatsThis( fileOpenText ) # Import File fileImportText = "<u><b>Import File</b></u><br>"\ "Inserts a file of any chemical file format supported by "\ "<b>Openbabel</b> into the current Part" win.fileImportAction.setWhatsThis(fileImportText) #Export File fileExportText = "<u><b>Export File</b></u><br>"\ "Save the current Part in any chemical file format supported by "\ "<b>Openbabel</b>. Note that exclusive features of NanoEngineer-1 "\ "are not saved to the exported file" win.fileExportAction.setWhatsThis(fileExportText) # Save File fileSaveText = "<u><b>Save File</b></u> (Ctrl + S)<br> "\ "<p><img source=\"ui/actions//Save.png\"><br> "\ "Saves the current file."\ "</p>" win.fileSaveAction.setWhatsThis( fileSaveText ) # # Edit Toolbar # # Make Checkpoint ### editMakeCheckpointText = \ "<u><b>Make Checkpoint</b></u>"\ "<p>"\ "<img source=\"ui/actions/Edit/Make_CheckPoint.png\"><br> "\ "Make Undo checkpoint."\ "</p>" win.editMakeCheckpointAction.setWhatsThis( editMakeCheckpointText ) # Automatic Checkpointing ### [minor changes, bruce 060319] editAutoCheckpointingText = \ "<u><b>Automatic Checkpointing</b></u>"\ "<p>"\ "Enables/Disables <b>Automatic Checkpointing</b>. When enabled, "\ "the program maintains the Undo stack automatically. When disabled, "\ "the user is required to manually create Undo checkpoints using the "\ "<b>Make Checkpoint</b> button: "\ "</p>"\ "<p><img source=\"ui/actions/Edit/Make_CheckPoint.png\">"\ "</p>"\ "<p><b>Automatic Checkpointing</b> can impact program performance. "\ "By disabling Automatic Checkpointing, the program will run faster. "\ "</p>"\ "<p><b><i>Remember that you must make your own Undo checkpoints "\ "manually when Automatic Checkpointing is disabled.</i></b>"\ "</p>" win.editAutoCheckpointingAction.setWhatsThis( editAutoCheckpointingText ) # Clear Undo Stack ### [minor changes, bruce 060319] editClearUndoStackText = "<u><b>Clear Undo Stack</b></u>"\ "<p>Clears all checkpoints on the Undo and Redo stacks, freeing up memory."\ "</p>" win.editClearUndoStackAction.setWhatsThis( editClearUndoStackText ) # Undo editUndoText = "<u><b>Undo</b></u> (Ctrl + Z)<br> "\ "<p><img source=\"ui/actions/Undo.png\"><br> "\ "Reverses the last edit or command which changed structure or selection. "\ "<br><font color=\"#808080\">"\ "Known bug: the link to wiki help for Undo "\ "only works if you got this popup from the Edit menu item for Undo, "\ "not from the Undo toolbutton."\ "</font>"\ "</p>" #bruce 060317 revised this text to reflect what it does in A7; 060320 added 1421-not-fixed warning win.editUndoAction.setWhatsThis( editUndoText ) win.editUndoText = editUndoText #bruce 060317 to help fix bug 1421 in Undo whatsthis wiki help link # Redo from PlatformDependent import is_macintosh if is_macintosh(): redo_accel = "(Ctrl + Shift + Z)" # note: this is further modified (Ctrl -> Cmd) by other code # changing this is partly redundant with code in undo*.py, but as of 060317 it's desirable in editRedoText too else: redo_accel = "(Ctrl + Y)" editRedoText = "<u><b>Redo</b></u> %s<br> "\ "<p><img source=\"ui/actions/Edit/Redo.png\"> <br>"\ "Restores a change which was undone using the Undo command."\ "<br><font color=\"#808080\">"\ "Known bug: the link to wiki help for Redo "\ "only works if you got this popup from the Edit menu item for Redo, "\ "not from the Redo toolbutton."\ "</font>"\ "</p>" % redo_accel #bruce 060317 revised this text to be more accurate, and split out redo_accel; 060320 added 1421-not-fixed warning win.editRedoAction.setWhatsThis( editRedoText ) win.editRedoText = editRedoText #bruce 060317 to help fix bug 1421 in Redo whatsthis wiki help link # Cut editCutText = "<u><b>Cut</b></u> (Ctrl + X)<br> "\ "<p><img source=\"ui/actions/Edit/Cut.png\"><br> "\ "Removes the selected object(s) and stores the cut data on the"\ "clipboard."\ "</p>" win.editCutAction.setWhatsThis( editCutText ) # Copy editCopyText = "<u><b>Copy</b></u> (Ctrl + C)<br> "\ "<p><img source=\"ui/actions/Edit/Copy.png\"><br> "\ "Places a copy of the selected chunk(s) on the clipboard "\ "while leaving the original chunk(s) unaffected."\ "</p>" win.editCopyAction.setWhatsThis( editCopyText ) # Paste editPasteText = "<u><b>Paste</b></u> (Ctrl + V)<br> "\ "<p><img source=\"ui/actions/Edit/Paste_On.png\"><br> "\ "<b>Paste</b> places the user in <b>Build</b> mode where copied chunks on "\ "the clipboard can be pasted into the model by double clicking in empty space. "\ "If the current clipboard chunk has a <b><i>hotspot</i></b>, it can be bonded to "\ "another chunk by single clicking on one of the chunk's bondpoints."\ "</p>"\ "<p>A <b><i>Hotspot</i></b> is a green bondpoint on a clipboard chunk indicating "\ "it will be the active bondpoint which will connect to another chunk's bondpoint. "\ "To specify a hotspot on the clipboard chunk, click on one of its bondpoints in the "\ "<b><i>MMKit's Thumbview</i></b>."\ "</p>" win.editPasteAction.setWhatsThis( editPasteText ) # Delete editDeleteText = "<u><b>Delete</b></u> (DEL)<br> "\ "<p><img source=\"ui/actions/Delete.png\"><br> "\ "Deletes the selected object(s). "\ "For this Alpha release, deleted objects may be permanently lost, or they might be recoverable using Undo.</p>" #bruce 060212 revised above text (and fixed spelling error); should be revised again before A7 release win.editDeleteAction.setWhatsThis( editDeleteText ) #Preferences Dialog editPrefsText = "<u><b>Preferences Dialog</b></u>"\ "<p>Allows you to edit various user preferences "\ "such as changing atom, bond display properties,"\ "lighting, background color, window position and"\ "size, plugins etc. </p>" win.editPrefsAction.setWhatsThis( editPrefsText ) # # View Toolbar # # Home View setViewHomeActionText = \ "<u><b>Home</b></u> (Home)<br>"\ "<p>"\ "<img source=\"ui/actions/View/Modify/Home.png\"><br>"\ "When you create a new model, it appears in a "\ "default view orientation (FRONT view). When you "\ "open an existing model, it appears in the "\ "orientation it was last saved. You can change the "\ "default orientation by selecting <b>Set Home View "\ "to Current View</b> from the <b>View</b> menu."\ "</p>" win.setViewHomeAction.setWhatsThis( setViewHomeActionText ) # Fit to Window setViewFitToWindowActionText = "<u><b>Fit To Window</b></u><br>"\ "<p><img source=\"ui/actions/View/Modify/Zoom_To_Fit.png\"><br> "\ "Refits the model to the screen so you can view the entire model."\ "</p>" win.setViewFitToWindowAction.setWhatsThis( setViewFitToWindowActionText ) # Recenter setViewRecenterActionText = "<u><b>Recenter</b></u><br>"\ "<p><img source=\"ui/actions/View/Modify/Recenter.png\"><br> "\ "Changes the view center and zoom factor so that the origin is in the "\ "center of the view and you can view the entire model."\ "</p>" win.setViewRecenterAction.setWhatsThis( setViewRecenterActionText ) # Zoom Tool setzoomToolActionText = "<u><b>Zoom Tool</b></u><br>"\ "<p><img source=\"ui/actions/View/Modify/Zoom.png\"><br> "\ "Allows the user to zoom into a specific area of the model by specifying a rectangular area. "\ "This is done by holding down the left button and dragging the mouse.</p>"\ "<p>A mouse with a mouse wheel can also be used to zoom in and out "\ "at any time, without using the Zoom Tool.</p>" win.zoomToolAction.setWhatsThis( setzoomToolActionText ) # Pan Tool setpanToolActionText = "<u><b>Pan Tool</b></u><br>"\ "<p><img source=\"ui/actions/View/Modify/Pan.png\"><br> "\ "Allows X-Y panning using the left mouse button.</p>"\ "<p>Users with a 3-button mouse can pan the model at any time by pressing "\ "the middle mouse button while holding down the Shift key.</p>" win.panToolAction.setWhatsThis( setpanToolActionText ) # Rotate Tool setrotateToolActionText = "<u><b>Rotate Tool</b></u><br>"\ "<p><img source=\"ui/actions/View/Modify/Rotate.png\"><br> "\ "Allows free rotation using the left mouse button.</p>"\ "<p>Users with a 3-button mouse can rotate the model at any time by pressing "\ "the middle mouse button and dragging the mouse.</p>" win.rotateToolAction.setWhatsThis( setrotateToolActionText ) # Orthographic Projection setViewOrthoActionText = "<u><b>Orthographic Projection</b></u><br>"\ "<p>Sets nonperspective (or parallel) projection, with no foreshortening."\ "</p>" win.setViewOrthoAction.setWhatsThis( setViewOrthoActionText ) # Perspective Projection setViewPerspecActionText = "<u><b>Perspective Projection</b></u><br>"\ "<p>Set perspective projection, drawing objects slightly larger "\ "that are closer to the viewer."\ "</p>" win.setViewPerspecAction.setWhatsThis( setViewPerspecActionText ) # Normal To viewNormalToActionText = "<u><b>Set View Normal To</b></u><br>"\ "<p><img source=\"ui/actions/View/Set_View_Normal_To.png/\"><br> "\ "Orients view to the normal vector of the plane defined by "\ "3 or more selected atoms, or a jig's axis."\ "</p>" win.viewNormalToAction.setWhatsThis( viewNormalToActionText ) # Parallel To viewParallelToActionText = "<u><b>Set View Parallel To</b></u><br>"\ "<p><img source=\"ui/actions/View/Set_View_Parallel_To.png\"><br> "\ "Orients view parallel to the vector defined by 2 selected atoms."\ "</p>" win.viewParallelToAction.setWhatsThis( viewParallelToActionText ) # Save Named View saveNamedViewActionText = "<u><b>Save Named View</b></u><br>"\ "<p><img source=\"ui/actions/View/Modify/Save_Named_View.png\"><br> "\ "Saves the current view as a custom <b>named view</b> and places it in the Model Tree.</p>" \ "<p>The view can be restored by selecting <b>Change View</b> from its context menu in the Model Tree."\ "</p>" win.saveNamedViewAction.setWhatsThis( saveNamedViewActionText ) # Front View viewFrontActionText = "<u><b>Front View</b></u><br>"\ "<p><img source=\"ui/actions/View/Front.png\"><br> "\ "Orients the view to the Front View."\ "</p>" win.viewFrontAction.setWhatsThis( viewFrontActionText ) # Back View viewBackActionText = "<u><b>Back View</b></u><br>"\ "<p><img source=\"ui/actions/View/Back.png\"><br> "\ "Orients the view to the Back View."\ "</p>" win.viewBackAction.setWhatsThis( viewBackActionText ) # Top View viewTopActionText = "<u><b>Top View</b></u><br>"\ "<p><img source=\"ui/actions/View/Top.png\"><br> "\ "Orients the view to the Top View."\ "</p>" win.viewTopAction.setWhatsThis( viewTopActionText ) # Bottom View viewBottomActionText = "<u><b>Bottom View</b></u><br>"\ "<p><img source=\"ui/actions/View/Bottom.png\"><br> "\ "Orients the view to the Bottom View."\ "</p>" win.viewBottomAction.setWhatsThis( viewBottomActionText ) # Left View viewLeftActionText = "<u><b>Left View</b></u><br>"\ "<p><img source=\"ui/actions/View/Left.png\"><br> "\ "Orients the view to the Left View."\ "</p>" win.viewLeftAction.setWhatsThis( viewLeftActionText ) # Right View viewRightActionText = "<u><b>Right View</b></u><br>"\ "<p><img source=\"ui/actions/View/Right.png\"><br> "\ "Orients the view to the Right View."\ "</p>" win.viewRightAction.setWhatsThis( viewRightActionText ) #Isometric View viewIsometricActionText = "<u><b>IsometricView</b></u><br>"\ "<p><img source=\"ui/actions/View/Isometric.png\"><br> "\ "Orients the view to the Isometric View."\ "</p>" win.viewIsometricAction.setWhatsThis( viewIsometricActionText ) # Rotate View 180 viewRotate180ActionText = "<u><b>Rotate View 180</b></u><br>"\ "<p><img source=\"ui/actions/View/Rotate_View_180.png.png\"><br> "\ "Rotates the view 180 degrees."\ "</p>" win.viewRotate180Action.setWhatsThis( viewRotate180ActionText ) # Rotate View +90 viewRotatePlus90ActionText = "<u><b>Rotate View +90</b></u><br>"\ "<p><img source=\"ui/actions/View/Rotate_View_+90.png\"><br> "\ "Increment the current view by 90 degrees around the vertical axis."\ "</p>" win.viewRotatePlus90Action.setWhatsThis( viewRotatePlus90ActionText ) # Rotate View -90 viewRotateMinus90ActionText = "<u><b>Rotate View -90</b></u><br>"\ "<p><img source=\"ui/actions/View/Rotate_View_-90.png\"><br> "\ "Decrement the current view by 90 degrees around the vertical axis."\ "</p>" win.viewRotateMinus90Action.setWhatsThis( viewRotateMinus90ActionText ) # QuteMol viewQuteMolActionText = \ "<u><b>QuteMol</b></u><br>"\ "<p><img source=\"ui/actions/View/Display/QuteMol.png\"><br> "\ "Starts QuteMol and loads a PDB file of the current model."\ "</p>" \ "QuteMol must be installed and enabled as a plug-in from "\ "<b>Preferences > Plug-ins</b> for this feature to work." \ "</p>" win.viewQuteMolAction.setWhatsThis( viewQuteMolActionText ) # POV-Ray (was Raytrace Scene) viewRaytraceSceneActionText = "<u><b>POV-Ray</b></u><br>"\ "<p><img source=\"ui/actions/View/Display/Raytrace_Scene.png\"><br> "\ "Raytrace the current scene using POV-Ray. "\ "</p>" \ "POV-Ray must be installed and enabled as a plug-in from "\ "<b>Preferences > Plug-ins</b> for this feature to work." \ "</p>" win.viewRaytraceSceneAction.setWhatsThis( viewRaytraceSceneActionText ) # # Grids Toolbar # # Surface 100 orient100ActionText = "<u><b>Surface 100</b></u><br>"\ "<p><img source=\"ui\actions\Properties Manager/Surface100.png\"><br> "\ "Reorients the view to the nearest angle that would "\ "look straight into a (1,0,0) surface of a diamond lattice."\ "</p>" win.orient100Action.setWhatsThis(orient100ActionText ) # Surface 110 orient110ActionText = "<u><b>Surface 110</b></u><br>"\ "<p><img source=\"ui\actions\Properties Manager/Surface110.png\"><br> "\ "Reorients the view to the nearest angle that would "\ "look straight into a (1,1,0) surface of a diamond lattice."\ "</p>" win.orient110Action.setWhatsThis(orient110ActionText ) # Surface 111 orient111ActionText = "<u><b>Surface 111</b></u><br>"\ "<p><img source=\"ui\actions\Properties Manager/Surface111.png\"><br> "\ "Reorients the view to the nearest angle that would "\ "look straight into a (1,1,1) surface of a diamond lattice."\ "</p>" win.orient111Action.setWhatsThis(orient111ActionText ) # # Insert toolbar # # Graphene insertGrapheneActionText = \ "<u><b>Build Graphene</b></u><br>"\ "<p><img source=\"ui/actions/Tools/Build Structures/Graphene.png\"><br> "\ "Inserts a 2D sheet of graphene in the model "\ "based on the current parameters in the Property Manager. "\ "To preview the structure based on the current parameters, "\ "click the Preview button located at the top of the "\ "Property Manager :<br> "\ "<img source=\"ui/actions/Properties Manager/Preview.png\"> "\ "</p>" win.insertGrapheneAction.setWhatsThis(insertGrapheneActionText ) # Build Nanotube insertNanotubeActionText = \ "<u><b>Build Nanotube</b></u>"\ "<p><img source=\"ui/actions/Tools/Build Structures/Nanotube.png\"> <br>"\ "Inserts a carbon or boron nitride nanotube in the model "\ "based on the current parameters in the Property Manager. "\ "To preview the structure based on the current parameters, "\ "click the Preview button located at the top of the "\ "Property Manager :<br> "\ "<img source=\"ui/actions/Properties Manager/Preview.png\"> "\ "</p>" win.insertNanotubeAction.setWhatsThis(insertNanotubeActionText ) # Build DNA buildDnaActionText = \ "<u><b>Build DNA</b></u><br>"\ "<p><img source=\"ui/actions/Tools/Build Structures/DNA.png\"><br> "\ "Inserts DNA in the model "\ "based on the current parameters in the Property Manager. "\ "To preview the structure based on the current parameters, "\ "click the Preview button located at the top of the "\ "Property Manager :<br> "\ "<img source=\"ui/actions/Properties Manager/Preview.png\"> "\ "</p>" win.buildDnaAction.setWhatsThis(buildDnaActionText ) # POV-Ray Scene insertPovraySceneActionText = "<u><b>Insert POV-Ray Scene</b></u><br>"\ "<p><img source=\"ui/actions/POV-Ray_Scene.png\"><br> "\ "Inserts a POV-Ray Scene file based on the current model and viewpoint. "\ "</p>" win.insertPovraySceneAction.setWhatsThis(insertPovraySceneActionText ) # Comment insertCommentActionText = "<u><b>Insert Comment</b></u><br>"\ "<p><img source=\"ui/actions/Insert/Comment.png\"><br> "\ "Inserts a comment in the current part. "\ "</p>" win.insertCommentAction.setWhatsThis(insertCommentActionText ) # # Display toolbar # # Display Default dispDefaultActionText = "<u><b>Display Default</b></u><br>"\ "<p><img source=\"ui/actions/View/Display/Default.png\"><br> "\ "Changes the <i>display setting</i> of selected atoms or chunks to "\ "<b>Default</b> , rendering them in the <b>Current Display Mode</b>."\ "</p>"\ "<p>If no atoms or chunks are selected, then this action will change the "\ "<b>Current Display Mode</b> of the 3D workspace to the <b>Default Display Mode</b>. " \ "All chunks with their display setting set to <b>Default</b> will be rendered in the "\ "<b>Default Display Mode</b>."\ "</p>"\ "<p>The <b>Default Display Mode</b> can be changed via the "\ "<b>Edit > Preferences</b> menu and selecting the <b>Modes</b> tab."\ "</p>"\ "<p>The <b>Current or Default Display Mode</b> is displayed in the status bar in the "\ "lower right corner of the main window."\ "</p>" win.dispDefaultAction.setWhatsThis(dispDefaultActionText ) # Display Invisible dispInvisActionText = "<u><b>Display Invisible</b></u><br>"\ "<p><img source=\"ui/actions/View/Display/Invisible.png\"><br> "\ "Changes the <i>display setting</i> of selected atoms or chunks to "\ "<b>Invisible</b>, making them invisible."\ "</p>"\ "<p>If no atoms or chunks are selected, then this action will change the "\ "<b>Current Display Mode</b> of the 3D workspace to <b>Invisible</b>. " \ "All chunks with their display setting set to <b>Default</b> will inherit "\ "this display property."\ "</p>" win.dispInvisAction.setWhatsThis(dispInvisActionText ) # Display Lines dispLinesActionText = "<u><b>Display Lines</b></u><br>"\ "<p><img source=\"ui/actions/View/Display/Lines.png\"><br> "\ "Changes the <i>display setting</i> of selected atoms or chunks to "\ " <b>Lines</b>. Only bonds are rendered as colored lines."\ "</p>"\ "<p>If no atoms or chunks are selected, then this action will change the "\ "<b>Current Display Mode</b> of the 3D workspace to <b>Lines</b>. " \ "All chunks with their display setting set to <b>Default</b> will inherit "\ "this display property."\ "</p>" win.dispLinesAction.setWhatsThis(dispLinesActionText ) # Display Tubes dispTubesActionText = "<u><b>Display Tubes</b></u><br>"\ "<p><img source=\"ui/actions/View/Display/Tubes.png\"><br> "\ "Changes the <i>display setting</i> of selected atoms or chunks to "\ "<b>Tubes</b>. Atoms and bonds are rendered as colored tubes."\ "</p>"\ "<p>If no atoms or chunks are selected, then this action will change the "\ "<b>Current Display Mode</b> of the 3D workspace to <b>Tubes</b>. " \ "All chunks with their display setting set to <b>Default</b> will inherit "\ "this display property."\ "</p>" win.dispTubesAction.setWhatsThis(dispTubesActionText ) # Display Ball and Stick dispBallActionText = "<u><b>Display Ball and Stick</b></u><br>"\ "<p><img source=\"ui/actions/View/Display/Ball_and_Stick.png\"><br> "\ "Changes the <i>display setting</i> of selected atoms or chunks to "\ "<b>Ball and Stick</b> mode. Atoms are rendered "\ "as spheres and bonds are rendered as narrow cylinders."\ "</p>"\ "<p>If no atoms or chunks are selected, then this action will change the "\ "<b>Current Display Mode</b> of the 3D workspace to <b>Ball and Stick</b>. " \ "All chunks with their display setting set to <b>Default</b> will inherit "\ "this display property."\ "</p>"\ "<p>The scale of the spheres and cylinders can be changed from the "\ "<b>Atoms</b> and <b>Bonds</b> pages of the <b>Preferences</b> dialog."\ "</p>" win.dispBallAction.setWhatsThis(dispBallActionText ) # Display CPK # [bruce extended and slightly corrected text, 060307] dispCPKActionText = "<u><b>Display CPK</b></u><br>"\ "<p><img source=\"ui/actions/View/Display/CPK.png\"><br> "\ "Changes the <i>display setting</i> of selected atoms or chunks to "\ "<b>CPK</b> mode. Atoms are rendered as spheres with "\ "a size equal to 0.78 of their VdW radius, corresponding "\ "to a contact force of approximately 0.1 nN with neighboring "\ "nonbonded atoms. Bonds are not rendered."\ "</p>"\ "<p>If no atoms or chunks are selected, then this action will change the "\ "<b>Current Display Mode</b> of the 3D workspace to <b>CPK</b>. " \ "All chunks with their display setting set to <b>Default</b> will inherit "\ "this display property."\ "</p>"\ "<p>The scale of the spheres can be changed from the "\ "<b>Atoms</b> and <b>Bonds</b> pages of the <b>Preferences</b> dialog."\ "</p>" win.dispCPKAction.setWhatsThis(dispCPKActionText ) # Display Cylinder dispCylinderActionText = "<u><b>Display Cylinder</b></u><br>"\ "<p><img source=\"ui/actions/View/Display/Cylinder.png\"><br> "\ "Changes the <i>display setting</i> of selected chunks to "\ "<b>Cylinder</b> mode. Chunks are rendered as cylinders."\ "</p>"\ "<p>If no chunks are selected, then this action will change the "\ "<b>Current Display Mode</b> of the 3D workspace to <b>Cylinder</b>. " \ "All chunks with their display setting set to <b>Default</b> will inherit "\ "this display property."\ "</p>" win.dispCylinderAction.setWhatsThis(dispCylinderActionText ) # Display Surface dispSurfaceActionText = "<u><b>Display Surface</b></u><br>"\ "<p><img source=\"ui/actions/View/Display/Surface.png\"><br> "\ "Changes the <i>display setting</i> of selected chunks to "\ "<b>Surface</b> mode. Chunks are rendered as a smooth surface."\ "</p>"\ "<p>If no chunks are selected, then this action will change the "\ "<b>Current Display Mode</b> of the 3D workspace to <b>Surface</b>. " \ "All chunks with their display setting set to <b>Default</b> will inherit "\ "this display property."\ "</p>" win.dispSurfaceAction.setWhatsThis(dispSurfaceActionText ) #Reset Chunk Color dispResetChunkColorText = "<u><b>Reset Chunk Color</b></u><br>"\ "Resets the user defined chunk color and renders the atoms " \ "(in the chunk) with their own element colors" win.dispResetChunkColorAction.setWhatsThis(dispResetChunkColorText ) #Reset Atoms Display dispResetAtomsDisplayText = "<u><b>Reset Atoms Display</b></u><br>"\ "Renders the selected atoms (or the atoms in the"\ "selected chunks) with the same display style as "\ "that of their parent chunk" win.dispResetAtomsDisplayAction.setWhatsThis(dispResetAtomsDisplayText) #Show Invisible Atoms dispShowInvisAtomsText = "<u><b>Show Invisible Atoms</b></u><br>"\ "Renders the selected atoms (or the atoms in the selected "\ "chunks) with the same display style as their parent chunk. "\ "However, if the parent chunk is set as invisible, this feature " \ "will not work. " win.dispShowInvisAtomsAction.setWhatsThis(dispShowInvisAtomsText) #Element Color Settings Dialog dispElementColorSettingsText = "<u><b>Element Color Settings Dialog</b></u><br>"\ "Element colors can be manually changed " \ "using this dialog. Also, the user can load"\ "or save the element colors" win.dispElementColorSettingsAction.setWhatsThis(dispElementColorSettingsText) # # Select toolbar # # Select All selectAllActionText = "<u><b>Select All</b></u> (Ctrl + A)<br>"\ "<p><img source=\"ui/actions/Tools/Select/Select_All.png\"><br> "\ "When in <b>Build</b> mode, this will select all the atoms in "\ "the model. Otherwise, this will select all the chunks in the model."\ "</p>" win.selectAllAction.setWhatsThis(selectAllActionText ) # Select None selectNoneActionText = "<u><b>Select None</b></u></p><br>"\ "<p><img source=\"ui/actions/Tools/Select/Select_None.png\"><br> "\ "Unselects everything currently selected.</p>" win.selectNoneAction.setWhatsThis(selectNoneActionText ) # InvertSelection selectInvertActionText = "<u><b>Invert Selection</b></u> (Ctrl + Shift + I)<br>"\ "<p><img source=\"ui/actions/Tools/Select/Select_Invert.png\"><br> "\ "Inverts the current selection.</p>" win.selectInvertAction.setWhatsThis(selectInvertActionText ) # Select Connected selectConnectedActionText = "<u><b>Select Connected</b></u> (Ctrl + Shift + C)<br>"\ "<p><img source=\"ui/actions/Tools/Select/Select_Connected.png\"><br> "\ "Selects all the atoms that can be reached by the currently selected atom "\ "via an unbroken chain of bonds. </p>"\ "<p>You can also select all connected atoms by double clicking on an atom or bond "\ "while in <b>Build</b> mode.</p>" win.selectConnectedAction.setWhatsThis(selectConnectedActionText ) # Select Doubly selectDoublyActionText = "<u><b>Select Doubly</b></u><br>"\ "<p><img source=\"ui/actions/Tools/Select/Select_Doubly.png\"><br> "\ "Selects all the atoms that can be reached from a currently selected "\ "atom through two disjoint unbroken chains of bonds. Atoms singly "\ "connected to this group and unconnected to anything else are also "\ "included in the selection."\ "</p>" win.selectDoublyAction.setWhatsThis(selectDoublyActionText ) # Expand Selection selectExpandActionText = "<u><b>Expand Selection</b></u> (Ctrl + D)<br>"\ "<p><img source=\"ui/actions/Tools/Select/Expand.png\"><br> "\ "Selects any atom that is a neighbor of a currently selected atom."\ "</p>" win.selectExpandAction.setWhatsThis(selectExpandActionText ) # Contract Selection selectContractActionText = "<u><b>Contract Selection</b></u> (Ctrl + Shift + D)<br>"\ "<p><img source=\"ui/actions/Tools/Select/Contract.png\"><br> "\ "Deselects any atom that is a neighbor of a non-picked atom or has a bondpoint."\ "</p>" win.selectContractAction.setWhatsThis(selectContractActionText ) # # Modify Toolbar # # Adjust Selection modifyAdjustSelActionText = "<u><b>Adjust Selection</b></u><br>"\ "<p><img source=\"ui/actions/Tools/Adjust_Selection.png\"><br> "\ "Adjusts the atom and bond positions (<i>of the selection</i>) to make the geometry more realistic. "\ "The operations used to move the atoms and bonds approximate molecular mechanics methods."\ "</p>" win.modifyAdjustSelAction.setWhatsThis(modifyAdjustSelActionText ) # Adjust All modifyAdjustAllActionText = "<u><b>Adjust All</b></u><br>"\ "<p><img source=\"ui/actions/Tools/Adjust_All.png\"><br> "\ "Adjusts the atom and bond positions (<i>of the entire part</i>) to make the geometry of the part more realistic. "\ "The operations used to move the atoms and bonds approximate molecular mechanics methods."\ "</p>" win.modifyAdjustAllAction.setWhatsThis(modifyAdjustAllActionText ) # Hydrogenate modifyHydrogenateActionText = "<u><b>Hydrogenate</b></u> <br>"\ "<p><img source=\"ui/actions/Tools/Build Tools/Hydrogenate.png\"><br> "\ "Adds hydrogen atoms to all the bondpoints in the selection.</p>" win.modifyHydrogenateAction.setWhatsThis(modifyHydrogenateActionText ) # Dehydrogenate modifyDehydrogenateActionText = "<u><b>Dehydrogenate</b></u><br>"\ "<p><img source=\"ui/actions/Tools/Build Tools/Dehydrogenate.png\"><br> "\ "Removes all hydrogen atoms from the selection.</p>" win.modifyDehydrogenateAction.setWhatsThis(modifyDehydrogenateActionText ) # Passivate modifyPassivateActionText = "<u><b>Passivate</b></u> (Ctrl + P)<br>"\ "<p><img source=\"ui/actions/Tools/Build Tools/Passivate.png\"><br> "\ "Changes the types of incompletely bonded atoms to atoms with the "\ "right number of bonds, using atoms with the best atomic radius."\ "</p>" win.modifyPassivateAction.setWhatsThis(modifyPassivateActionText ) # Stretch modifyStretchActionText = "<u><b>Stretch</b></u><br>"\ "<p><img source=\"ui/actions/Tools/Build Tools/Stretch.png\"><br> "\ "Stretches the bonds of the selected chunk(s).</p>" win.modifyStretchAction.setWhatsThis(modifyStretchActionText ) # Delete Bonds modifyDeleteBondsActionText = "<u><b>Cut Bonds</b></u><br>"\ "<p><img source=\"ui/actions/Tools/Build Tools/Delete_Bonds.png\"><br> "\ "Delete all bonds between selected and unselected atoms or chunks.</p>" win.modifyDeleteBondsAction.setWhatsThis(modifyDeleteBondsActionText ) # Separate/New Chunk modifySeparateActionText = "<u><b>Separate</b></u><br>"\ "<p><img source=\"ui/actions/Tools/Build Tools/Separate.png\"><br> "\ "Creates a new chunk(s) from the currently selected atoms. "\ "If the selected atoms belong to different chunks, multiple new "\ "chunks are created.</p>" win.modifySeparateAction.setWhatsThis(modifySeparateActionText ) # New Chunk makeChunkFromSelectedAtomsActionText = "<u><b>New Chunk</b></u><br>"\ "<p><img source=\"ui/actions/Tools/Build Tools/New_Chunk.png\"><br> "\ "Creates a new chunk from the currently selected atoms. "\ "All atoms end up in a single chunk.</p>" win.makeChunkFromSelectedAtomsAction.setWhatsThis(makeChunkFromSelectedAtomsActionText ) # Merge Chunks modifyMergeActionText = "<u><b>Merge Chunks</b></u><br>"\ "<p><img source=\"ui/actions/Tools/Build Tools/Merge.png\"><br> "\ "Merges two or more chunks into a single chunk.</p>" win.modifyMergeAction.setWhatsThis(modifyMergeActionText ) # Invert Chunks modifyInvertActionText = "<u><b>Invert</b></u><br>"\ "<p><img source=\"ui/actions/Tools/Build Tools/Invert.png\"><br> "\ "Inverts the atoms of the selected chunks.</p>" win.modifyInvertAction.setWhatsThis(modifyInvertActionText ) # Mirror Selected Chunks #Note that the the feature name is intentionally kept "Mirror" instead of "Mirror Chunks" because # in future we will support mirrroing atoms as well. -- ninad060814 modifyMirrorActionText = "<u><b>Mirror</b></u><br>"\ "<p><img source=\"ui/actions/Tools/Build Tools/Mirror.png\"><br> "\ "Mirrors the selected <b> chunks </b> about a reference Grid Plane.<br>"\ "<font color=\"#808080\">Note: In this version, it doesn't mirror jigs or individual atoms.</font> </p>" win.modifyMirrorAction.setWhatsThis(modifyMirrorActionText ) # Align to Common Axis modifyAlignCommonAxisActionText = "<u><b>Align To Common Axis</b></u><br>"\ "<p><img source=\"ui/actions/Tools/Build Tools/AlignToCommonAxis.png\"><br> "\ "Aligns one or more chunks to the axis of the first selected chunk."\ "You must select two or more chunks before using this feature."\ "</p>" win. modifyAlignCommonAxisAction.setWhatsThis( modifyAlignCommonAxisActionText ) #Center on Common Axis modifyCenterCommonAxisActionText= "<u><b>Center On Common Axis</b></u><br>"\ "<p><b> Moves</b> all selected chunks to the center of the <b> first </b> selected chunk "\ "and also <b>aligns</b> them to the axis of the first one ."\ "You must select two or more chunks before using this feature. </p>" win.modifyCenterCommonAxisAction.setWhatsThis(modifyCenterCommonAxisActionText) # # Tools Toolbar # # Select Chunks toolsSelectMoleculesActionText = "<u><b>Select Chunks</b></u><!-- [[Feature:Select Chunks Mode]] --><br>"\ "<p><img source=\"ui/actions/Toolbars/Standard/63.png\"><br> "\ "<b>Select Chunks</b> allows you to select/unselect chunks with the mouse.</p>"\ "<p><b><u>Mouse/Key Combinations</u></b></p>"\ "<p><b>Left Click/Drag</b> - selects a chunk(s).</p>"\ "<p><b>Ctrl+Left Click/Drag</b> - removes chunk(s) from selection.</p>"\ "<p><b>Shift+Left Click/Drag</b> - adds chunk(s) to selection."\ "</p>" win. toolsSelectMoleculesAction.setWhatsThis( toolsSelectMoleculesActionText ) # Move Chunks toolsMoveMoleculeActionText = "<u><b>Move Chunks</b></u><!-- [[Feature:Move Chunks Mode]] --><br>"\ "<p><img source=\"ui/actions/Toolbars/Standard/64.png\"><br> "\ "Activates <b>Move Chunks</b> mode, allowing you to select, "\ "move and rotate one of more chunks with the mouse.</p>"\ "<p><b><u>Mouse/Key Combinations</u></b></p>"\ "<p><b>Left Drag</b> - moves the selected chunk(s).</p>"\ "<p><b>Ctrl+Left Drag</b> - freely rotates selected chunk(s).</p>"\ "<p><b>Shift+Left Drag</b> - constrained movement and rotation of a chunk about its own axis."\ "</p>" win. toolsMoveMoleculeAction.setWhatsThis( toolsMoveMoleculeActionText ) # Build Atoms toolsDepositAtomActionText = \ "<u><b>Build Atoms</b></u><!-- [[Feature:Build Atoms]] --><br>"\ "<p><img source=\"ui/actions/Tools/Build Structures/Atoms.png\"><br> "\ "<b>Build Atoms</b> allows you to build structures one atom at a time or by depositing objects "\ "that are on the paste clipboard. You can also insert structures from the "\ "NanoEngineer-1 Parts Library.</p>"\ "<p>It is also possible to change bond types between atoms using the <b>Bond Tool</b> or by "\ "simply dragging and dropping one bondpoint onto another."\ "</p>" win. toolsDepositAtomAction.setWhatsThis( toolsDepositAtomActionText ) # Build Crystal (was Cookie Cutter Mode) toolsCookieCutActionText = "<u><b>Build Crystal</b></u><!-- [[Feature:Build Crystal]] --><br>"\ "<p><><img source=\"ui/actions/Tools/Build Structures/Cookie_Cutter.png\"><br> "\ "<b>Build Crystal</b> provides tools for cutting out multi-layered shapes from "\ "slabs of diamond or lonsdaleite lattice.</p>" win. toolsCookieCutAction.setWhatsThis( toolsCookieCutActionText ) # Tools > Extrude toolsExtrudeActionText = "<u><b>Extrude</b></u><!-- [[Feature:Extrude Mode]] --><br>"\ "<p><img source=\"ui/actions/Insert/Features/Extrude.png\"><br> "\ "Activates <b>Extrude</b> mode, allowing you to create a rod or ring using a chunk as "\ "a repeating unit.</p>" win. toolsExtrudeAction.setWhatsThis( toolsExtrudeActionText ) # Fuse Chunks Mode toolsFuseChunksActionText = "<u><b>Fuse Chunks Mode</b></u><!-- [[Feature:Fuse Chunks Mode]] --><br>"\ "<p><img source=\"ui/actions/Tools/Build Tools/Fuse.png\"><br> "\ "<b>Fuse Chunks</b> can be used to interactively join two or more "\ "chunks by dragging chunks around and fusing them together. "\ "Two fusing options are supported:<br><br>"\ "<b>Make Bonds</b> creates bonds between the existing bondpoints "\ "of two or more chunks. Bondpoints are highlighted and lines are drawn (and undrawn) as chunks "\ "are dragged to indicate bonding relationships between bondpoints. Bondpoints with "\ "multiple bonding relationships are highlighted in magenta to indicate that they cannot "\ "make bonds.<br><br>"\ "<b>Fuse Atoms</b> fuses pairs of overlapping atoms between chunks. The set of overlapping "\ "atoms in the selected chunk(s) are highlighted in green while the set of atoms that will be deleted "\ "in non-selected chunks are highlighted in dark red. It is possible that deleted atoms will not fuse "\ "properly, leaving bondpoints on the selected chunk(s) atoms. This is a bug. To help "\ "minimize this problem, try to get the bonds of overlapping atoms oriented similarly.<br>"\ "</p>" win.toolsFuseChunksAction.setWhatsThis( toolsFuseChunksActionText ) # # Simulator Toolbar # # Minimize Energy simMinimizeEnergyActionText = "<u><b>Minimize Energy</b></u><br>"\ "<p><img source=\"ui/actions/Simulation/Minimize_Energy.png\"><br> "\ "The potential energy of a chemical structure is a function of the relative positions of its atoms. " \ "To obtain this energy with complete accuracy involves a lot of computer time spent on quantum " \ "mechanical calculations, which cannot be practically done on a desktop computer. "\ "To get an approximate potential energy without all that, we represent the energy as a series of " \ "terms involving geometric properties of the structure: lengths of chemical bonds, angles between " \ "pairs and triples of chemical bonds, etc. </p>" \ "<p>" \ "As is generally the case with physical systems, the gradient of the potential energy represents " \ "the forces acting on various particles. The atoms want to move in the direction that most reduces " \ "the potential energy. Energy minimization is a process of adjusting the atom positions to try to find " \ "a global minimum of the potential energy. Each atom contributes three variables (its x, y, and z " \ "coordinates) so the search space is multi-dimensional. The global minimum is the configuration " \ "that the atoms will settle into if lowered to zero Kelvin. </p>" win. simMinimizeEnergyAction.setWhatsThis( simMinimizeEnergyActionText ) # Run Dynamics (was NanoDynamics-1). Mark 060807. simSetupActionText = "<u><b>Run Dynamics</b></u><br>"\ "<p><img source=\"ui/actions/Simulation/Run_Dynamics.png\"><br> "\ "This is the interface to the NanoEngineer-1 molecular dynamics simulator. "\ "Enter the parameters of the simulation and click <b>Run Simulation</b>."\ "The simulator creates a trajectory (movie) file by calculating the inter-atomic potentials and bonding "\ "of the entire model.</p>" win. simSetupAction.setWhatsThis( simSetupActionText ) # Play Movie (was Movie Player) Mark 060807. simMoviePlayerActionText = "<u><b>Play Movie</b></u><br>"\ "<p><img source=\"ui/actions/Simulation/Play_Movie.png\"><br> "\ "Plays the most recent trajectory (movie) file created by the NanoEngineer-1 molecular dynamics simulator."\ "To create a movie file, select <b>Run Dynamics</b>.</p>" win. simMoviePlayerAction.setWhatsThis( simMoviePlayerActionText ) # Make Graphs (was Plot Tool) Mark 060807. simPlotToolActionText = "<u><b>Make Graphs</b></u><br>"\ "<p><img source=\"ui/actions/Simulation/Make_Graphs.png\"><br> "\ "Make a graph of a simulator trace file using GNUplot. A simulation must be run to create "\ "the trace file and the part must have a jig that writes output to the trace file. <br><br>"\ "The following list of jigs write data to the trace file:<br>"\ "<b>Rotary Motors:</b> speed (GHz) and torque (nn-nm)<br>"\ "<b>Linear Motors:</b> displacement (pm)<br>"\ "<b>Anchors:</b> torque (nn-nm)<br>"\ "<b>Thermostats:</b> energy added (zJ)<br>"\ "<b>Thermometer:</b> temperature (K)<br>"\ "<b>Measure Distance:</b> distance(angstroms)<br>"\ "<b>Measure Angle:</b> angle (degrees)<br>"\ "<b>Measure Dihedral:</b> dihedral(degrees)<br>"\ "</p>" win. simPlotToolAction.setWhatsThis( simPlotToolActionText ) # # Dashboard Buttons # # Done toolsDoneActionText = "<u><b>Done</b></u><br>"\ "<p><img source=\"ui/actions/Properties Manager/Done.png\"><br> "\ "Completes the current operation and enters the default mode."\ "</p>" win. toolsDoneAction.setWhatsThis( toolsDoneActionText ) # Cancel toolsCancelActionText = "<u><b>Cancel</b></u><br>"\ "<p><img source=\"ui/actions/Properties Manager/Cancel.png\"><br> "\ "Cancels the current operation and enters the default mode."\ "</p>" win. toolsCancelAction.setWhatsThis( toolsCancelActionText ) # Back up toolsBackUpActionText = "<u><b>Back Up</b></u><br>"\ "Undoes the previous operation."\ "</p>" win. toolsBackUpAction.setWhatsThis( toolsBackUpActionText ) # Start Over toolsStartOverActionText = "<u><b>Start Over</b></u><br>"\ "Cancels the current operation, leaving the user in the current mode."\ "</p>" win.toolsStartOverAction.setWhatsThis(toolsStartOverActionText ) # Add Layers ccAddLayerActionText = "<u><b>Add Layer</b></u><br>"\ "<p><img source=\"ui/actions/Properties Manager/addlayer.png\"><br> "\ "Adds a new layer of diamond lattice to the existing layer."\ "</p>" win.ccAddLayerAction.setWhatsThis(ccAddLayerActionText ) # # Jigs # # Anchor jigsAnchorActionText = "<u><b>Anchor</b></u><br>"\ "<p><img source=\"ui/actions/Simulation/Anchor.png\"><br> "\ "Attaches an <b>Anchor</b> to the selected atom(s), which "\ "constrains its motion during a minimization or simulation."\ "</p>"\ "<p>To create an Anchor, enter <b>Build</b> mode, "\ "select the atom(s) you want to anchor and then select this action. "\ "Anchors are drawn as a black wireframe box around each selected atom."\ "</p>" win.jigsAnchorAction.setWhatsThis(jigsAnchorActionText ) # Rotary Motor jigsMotorActionText = "<u><b>Rotary Motor</b></u><br>"\ "<p><img source=\"ui/actions/Simulation/Rotary_Motor.png\"><br> "\ "Attaches a <b>Rotary Motor</b> to the selected atoms. The Rotary Motor is used by "\ "the simulator to apply rotary motion to a set of atoms during a simulation run. You may "\ "specify the <b>torque (in nN*nm)</b> and <b>speed (in Ghz)</b> of the motor."\ "</p>"\ "<p>To create a Rotary Motor, enter <b>Build</b> mode, "\ "select the atoms you want to attach the motor to and then select this action."\ "</p>" win.jigsMotorAction.setWhatsThis(jigsMotorActionText ) # Linear Motor jigsLinearMotorActionText = "<u><b>Linear Motor</b></u><br>"\ "<p><img source=\"ui/actions/Simulation/Linear_Motor.png\"><br> "\ "Attaches a <b>Linear Motor</b> to the selected atoms. The Linear Motor is used by "\ "the simulator to apply linear motion to a set of atoms during a simulation run. You may "\ "specify the <b>force (in nN*nm)</b> and <b>stiffness (in N/m)</b> of the motor."\ "</p>"\ "<p>To create a Linear Motor, enter <b>Build</b> mode, "\ "select the atoms you want to attach the motor to and then select this action."\ "</p>" win.jigsLinearMotorAction.setWhatsThis(jigsLinearMotorActionText ) # Thermostat jigsStatActionText = "<u><b>Thermostat</b></u><br>"\ "<p><img source=\"ui/actions/Simulation/Thermostat.png\"><br> "\ "Attaches a <b>Langevin Thermostat</b> to a single selected atom, thereby associating "\ "the themostat to the entire molecule of which the selected atom is a member. The user "\ "specifies the temperature (in Kelvin)."\ "</p>"\ "<p>The Langevin Thermostat is used to set and hold the temperature "\ "of a molecule during a simulation run."\ "</p>"\ "<p>To create a Langevin Thermostat, enter <b>Build</b> mode, "\ "select a single atom and then select this action. The thermostat is drawn as a "\ "blue wireframe box around the selected atom."\ "</p>" win.jigsStatAction.setWhatsThis(jigsStatActionText ) # Thermometer jigsThermoActionText = "<u><b>Thermometer</b></u><br>"\ "<p><img source=\"ui/actions/Simulation/Measurements/Thermometer.png\"><br> "\ "Attaches a <b>Thermometer</b> to a single selected atom, thereby associating "\ "the themometer to the entire molecule of which the selected atom is a member. "\ "<p>The temperature of the molecule will be recorded and written to a trace file "\ "during a simulation run."\ "</p>"\ "<p>To create a Thermometer, enter <b>Build</b> mode, "\ "select a single atom and then select this action. The thermometer is drawn as a "\ "dark red wireframe box around the selected atom."\ "</p>" win.jigsThermoAction.setWhatsThis(jigsThermoActionText ) # ESP Image jigsESPImageActionText = "<u><b>ESP Image</b></u><br>"\ "<p><img source=\"ui/actions/Simulation/ESP_Image.png\"><br> "\ "An <b>ESP Image</b> allows the user to visualize the electrostatic potential "\ "of points on the face of a square 2D surface. Nano-Hive's MPQC ESP Plane plug-in "\ "is used to calculate the electrostatic potential."\ "</p>"\ "<p>To create an ESP Image, enter <b>Build</b> mode, "\ "select three or more atoms and then select this jig. The ESP Image is drawn as a "\ "plane with a bounding volume."\ "</p>" win.jigsESPImageAction.setWhatsThis(jigsESPImageActionText ) # Atom Set jigsAtomSetActionText = "<u><b>Atom Set</b></u><br>"\ "<p><img source=\"ui/actions/Tools/Atom_Set.png\"><br> "\ "An <b>Atom Set</b> jig provides a convienient way to save an atom "\ "selection which can be reselected later."\ "</p>"\ "<p>To create an Atom Set, enter <b>Build</b> mode, "\ "select any number of atoms and then select this jig. The Atom Set is "\ "drawn as a set of wireframe boxes around each atom in the selection."\ "</p>"\ "<p>To reselect the atoms in an Atom Set, select it's context "\ "menu in the Model Tree and click the menu item that states "\ "<b>Select this jig's atoms</b>."\ "</p>" win.jigsAtomSetAction.setWhatsThis(jigsAtomSetActionText ) # Measure Distance jigsDistanceActionText = "<u><b>Measure Distance Jig</b></u><br>"\ "<p><img source=\"ui/actions/Simulation/Measurements/Measure_Distance.png\"><br> "\ "A <b>Measure Distance Jig</b> functions as a dimension to display the "\ "distance between two atoms."\ "</p>"\ "<p>To create the Measure Distance Jig, enter <b>Build</b> mode, "\ "select two atoms and then select this jig. The Measure Distance Jig is "\ "drawn as a pair of wireframe boxes around each atom connected by "\ "a line and a pair of numbers. The first number is the distance between the "\ "VdW radii (this can be a negative number for atoms that are close together). "\ "The second number is the distance between the nuclei."\ "</p>"\ "<p>The Measure Distance Jig will write the two distance values to the trace file "\ "for each frame of a simulation run and can be plotted using the Plot Tool."\ "</p>" win.jigsDistanceAction.setWhatsThis(jigsDistanceActionText ) # Measure Angle jigsAngleActionText = "<u><b>Measure Angle Jig</b></u><br>"\ "<p><img source=\"ui/actions/Simulation/Measurements/Measure_Angle.png\"><br> "\ "A <b>Measure Angle Jig</b> functions as a dimension to display the "\ "angle between three atoms.</p>"\ "<p>To create the Measure Angle Jig, enter <b>Build</b> mode, "\ "select three atoms and then select this jig. The Measure Angle Jig is "\ "drawn as a set of wireframe boxes around each atom and a number "\ "which is the angle between the three atoms."\ "</p>"\ "<p>The Measure Angle Jig will write the angle value to the trace file "\ "for each frame of a simulation run and can be plotted using the Plot Tool."\ "</p>" win.jigsAngleAction.setWhatsThis(jigsAngleActionText ) # Measure Dihedral jigsDihedralActionText = "<u><b>Measure Dihedral Jig</b></u><br>"\ "<p><img source=\"ui/actions/Simulation/Measurements/Measure_Dihedral.png\"><br> "\ "A <b>Measure Dihedral Jig</b> functions as a dimension to display the "\ "dihedral angle of a four atom sequence.</p>"\ "<p>To create the Measure Dihedral Jig, enter <b>Build</b> mode, "\ "select four atoms and then select this jig. The Measure Dihedral Jig is "\ "drawn as a set of wireframe boxes around each atom and a number "\ "which is the dihedral angle value."\ "</p>"\ "<p>The Measure Dihedral Jig will write the dihedral angle value to the trace file "\ "for each frame of a simulation run and can be plotted using the Plot Tool."\ "</p>" win.jigsDihedralAction.setWhatsThis(jigsDihedralActionText ) # GAMESS Jig jigsGamessActionText = "<u><b>GAMESS Jig</b></u><br>"\ "<p><img source=\"ui/actions/Simulation/Gamess.png\"><br> "\ "A <b>GAMESS Jig</b> is used to tag a set of atoms for running a GAMESS "\ "calculation. <b>Energy</b> and <b>Geometry Optimization</b> calculations are supported."\ "</p>"\ "<p>To create the GAMESS Jig, enter <b>Build</b> mode, "\ "select the atoms to tag and then select this jig. The GAMESS Jig is drawn as a "\ "set of magenta wireframe boxes around each atom."\ "</p>" win.jigsGamessAction.setWhatsThis(jigsGamessActionText ) # Grid Plane Jig jigsGridPlaneActionText = "<u><b>Grid Plane</b></u><br>"\ "<p><img source=\"ui/actions/Insert/Reference Geometry/Grid_Plane.png\"><br> "\ "A <b>Grid Plane</b> jig is a rectanglar plane that can display a square or SiC grid "\ "within its boundary. It is often used as an aid in constructing large lattice "\ "structures made of silicon carbide (SiC). It is also used as a visual aid in estimating "\ "distances between atoms and/or other structures."\ "</p>"\ "<p>To create the Grid Plane jig, enter <b>Build</b> mode, "\ "select three or more atoms and then select this jig. "\ "</p>"\ "<p>The Grid Plane jig is drawn as a rectanglar plane with a grid."\ "</p>" win.jigsGridPlaneAction.setWhatsThis(jigsGridPlaneActionText ) # # Help Toolbar # # What's This helpWhatsThisText = "<u><b>What's This</b></u><br>"\ "<p><img source=\"ui/actions/Help/WhatsThis.png\"><br> "\ "Click this option to invoke a small question mark that is attached to the mouse pointer. "\ "Click on a feature which you would like more information about. "\ "A popup box appears with information about the feature.</p>" win.helpWhatsThisAction.setWhatsThis( helpWhatsThisText ) win.helpMouseControlsAction.setWhatsThis('Displays help for mouse controls') win.helpKeyboardShortcutsAction.setWhatsThis('Displays help for keyboard shortcuts') | 596540c24ceb3b478e904a42e26d7d5dd8809d95 /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/11221/596540c24ceb3b478e904a42e26d7d5dd8809d95/whatsthis.py | [
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elif os.path.isfile(connect_paths(libpath, '__init__.py')): mod.filename = connect_paths(libpath, '__init__.py') | elif os.path.isfile(connect_paths(libpath, '__init__.py')): mod.filename = libpath+'/__init__.py' | def parse_module(name, ast=None, parent=None, node=None): # --- valid name? for c in name: if not c in string.letters+string.digits+'_.': print ("*ERROR*:%s.py: module names should consist of letters, digits and underscores" % name) sys.exit() # --- parse ident = name.split('.')[-1] mod = module(ident, node) mod.builtin = False if ast: # XXX mod.ast = ast mod.filename = name+'.py' mod.dir = '' mod.mod_path = [name] mod.mod_dir = [] else: # --- locate module relname = name.replace('.', '/') relpath = name.split('.') if parent: path = connect_paths(parent.dir, relname) else: path = name libpath = connect_paths(getgx().libdir, relname) rootpath = connect_paths(os.getcwd(), relname) if os.path.isfile(path+'.py'): # local module mod.filename = path+'.py' if parent: mod.mod_path = parent.mod_dir + relpath else: mod.mod_path = relpath split = path.split('/') mod.dir = '/'.join(split[:-1]) mod.mod_dir = mod.mod_path[:-1] mod.builtin = not parent or parent.builtin elif os.path.isfile(connect_paths(path, '__init__.py')): mod.filename = connect_paths(path, '__init__.py') if parent: mod.mod_path = parent.mod_dir + relpath else: mod.mod_path = relpath mod.dir = path mod.mod_dir = mod.mod_path mod.builtin = not parent or parent.builtin elif os.path.isfile(rootpath+'.py'): # root module mod.filename = rootpath+'.py' mod.mod_path = relpath split = rootpath.split('/') mod.dir = '/'.join(split[:-1]) mod.mod_dir = mod.mod_path[:-1] elif os.path.isfile(connect_paths(rootpath, '__init__.py')): mod.filename = connect_paths(rootpath, '__init__.py') mod.mod_path = relpath mod.dir = rootpath mod.mod_dir = mod.mod_path elif os.path.isfile(libpath+'.py'): # library module mod.filename = libpath+'.py' mod.mod_path = relpath split = libpath.split('/') mod.dir = '/'.join(split[:-1]) mod.mod_dir = mod.mod_path[:-1] mod.builtin = True elif os.path.isfile(connect_paths(libpath, '__init__.py')): mod.filename = connect_paths(libpath, '__init__.py') mod.mod_path = relpath mod.dir = libpath mod.mod_dir = mod.mod_path mod.builtin = True else: error('cannot locate module: '+name, node) modpath = '.'.join(mod.mod_path) if modpath in getgx().modules: # cached? return getgx().modules[modpath] #print 'not cached', modpath getgx().modules[modpath] = mod mod.ast = parsefile(mod.filename) old_mv = getmv() mod.mv = mv = moduleVisitor(mod) setmv(mv) mv.visit = mv.dispatch mv.visitor = mv mv.dispatch(mod.ast) mv = old_mv setmv(mv) mod.funcs = mod.mv.funcs mod.classes = mod.mv.classes return mod | d7ff07b382c793e4aea86abd70975b573665754e /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/4470/d7ff07b382c793e4aea86abd70975b573665754e/graph.py | [
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FunctionnalTest(CHECK + [ "group", "-v", "--name=%s" % group_name ], context=context).Run() group_name = "groupe_a_skel" FunctionnalTest(ADD + [ "group", "--name=%s" % group_name, '''--description="Le groupe C s'il vous plaît..."''' ], context=context).Run() FunctionnalTest(MODIFY + [ "group", '--name=%s' % group_name, '--not-permissive' ], chk_cmds = [ gen_chk_acls_cmds(group_name) ], context=context).Run() FunctionnalTest(MODIFY + [ "group", "--name=%s" % group_name, "--permissive" ], chk_cmds = [ gen_chk_acls_cmds(group_name) ], context=context).Run() FunctionnalTest(MODIFY + [ "group", "--name=%s" % group_name, "--permissive" ], context=context+'+already').Run() | gname = 'ARCHIVES-test' ScenarioTest([ ADD + [ 'group', gname, '-v' ], [ 'sudo', 'touch', "%s/%s/%s/test.txt" % ( configuration.defaults.home_base_path, configuration.groups.names['plural'], gname) ], [ 'sudo', 'mkdir', "%s/%s/%s/testdir" % ( configuration.defaults.home_base_path, configuration.groups.names['plural'], gname) ], [ 'sudo', 'touch', "%s/%s/%s/testdir/testfile" % ( configuration.defaults.home_base_path, configuration.groups.names['plural'], gname) ], CHK + [ "group", "-vb", gname ], DEL + [ 'group', gname ], [ 'sudo', 'find', configuration.home_archive_dir ], [ 'sudo', 'getfacl', '-R', configuration.home_archive_dir ], [ 'sudo', 'rm', '-rf', '%s/*' % configuration.home_archive_dir ] ], context=context, descr='''verify the --archive option of DEL group and check on ''' '''shared dir contents.''' ).Run() | def gen_chk_acls_cmds(group): | 07cb13c975b820cb15074a8378ec89357e5846f4 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/7650/07cb13c975b820cb15074a8378ec89357e5846f4/core.py | [
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widget=TextAreaWidget(), | def generateFti(self,element,subtypes): ''' ''' | f5e5b424a0e01e9a88492672f53fc4444f4bee7f /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/11941/f5e5b424a0e01e9a88492672f53fc4444f4bee7f/ArchGenXML.py | [
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atomStart0 = chain[helix.startIndex-1].getAtom('CA') atomStart1 = chain[helix.startIndex].getAtom('CA') | if(helix.startIndex-1 in chain.residueRange()): atomStart0 = chain[helix.startIndex-1].getAtom('CA') if(helix.startIndex in chain.residueRange()): atomStart1 = chain[helix.startIndex].getAtom('CA') | def helixFlipButtonPress(self): """ | 21dad13f9a8161dface447e24aefbdaa6b79a129 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/4399/21dad13f9a8161dface447e24aefbdaa6b79a129/calpha_structure_editor.py | [
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error_handler=log.err) | error_handler=d.errback) | def get_charset2_cb(_charset): # check that the new charset is the expected one self.assertEqual(new_charset, _charset) # leave everything as found self.device.SetCharset(charset, dbus_interface=CRD_INTFACE, reply_handler=lambda: d.callback(True), error_handler=log.err) | 45c00959c14e666ef31b3f93137f14e6d66959e4 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/12036/45c00959c14e666ef31b3f93137f14e6d66959e4/test_dbus.py | [
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print 'Problem in %s - %s' % (value.filename, value.args) | print value | def doc(thing): """Display documentation on an object (for interactive use).""" if type(thing) is type(""): try: path, x = locate(thing) except DocImportError, value: print 'Problem in %s - %s' % (value.filename, value.args) return if x: thing = x else: print 'No Python documentation found for %s.' % repr(thing) return desc = describe(thing) module = inspect.getmodule(thing) if module and module is not thing: desc = desc + ' in module ' + module.__name__ pager('Help on %s:\n\n' % desc + text.document(thing)) | 37f7b38eb6247564c00c8a355ab12268e8486c4e /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/8546/37f7b38eb6247564c00c8a355ab12268e8486c4e/pydoc.py | [
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print "no dll" raise self.Exceptions.DeviceNotFound | raise self.Exceptions.DriverNotFound | def __start__( self, ledRX=True, ledTX=True, legacyRX=False, repeatStopCodes=False, | 8f7bce61609e1a37f6170e13dfa118b231e99f38 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/8076/8f7bce61609e1a37f6170e13dfa118b231e99f38/__init__.py | [
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self.assertEqual(u.fp._sock.fp._sock.gettimeout(), 120) | self.assertEqual(u.fp.raw.fp._sock.gettimeout(), 120) | def test_http_Value(self): u = urllib2.urlopen("http://www.python.org", timeout=120) self.assertEqual(u.fp._sock.fp._sock.gettimeout(), 120) | 9834ba99773dc9627749f716d360358387ae516b /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/12029/9834ba99773dc9627749f716d360358387ae516b/test_urllib2net.py | [
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""" | r""" | def encoding(self,S,padic=False): """ The binary encoding of the string S, as a binary string element. | ca219b0206186a194cdf8e11d2082bec654536f8 /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/9417/ca219b0206186a194cdf8e11d2082bec654536f8/string_monoid.py | [
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log.msg("Changing listening port in server.conf " + | log.msg("Changing listening port " + | def main(options): """ Main execution loop of the server. """ # config = get_conf('server') # LOG_FILE = config['log_file'] # LOG_LEVEL = config['log_level'] # SSL = get_bool(config['ssl']) # SSL_PRIVKEY = config['privkey_file'] # SSL_CERT = config['cert_file'] # CLIENT_PORT = int(config['client_port']) # PUBKEY_DATABASE = os.path.expanduser(config['pubkey_database']) # STATS_FILE = config['stats_file'] LOG_FILE = options.logfile LOG_LEVEL = options.loglevel SSL = get_bool(options.ssl) SSL_PRIVKEY = options.privkey SSL_CERT = options.cert CLIENT_PORT = options.port STATS_FILE = options.statsfile DB_FILE = options.dbfile FAILURE_THRESHOLD = options.job_failure_threshold # start logging startLogging(LOG_FILE) # Job database jobdb = JobDatabaseSQLite(db_file=DB_FILE, job_failure_threshold=FAILURE_THRESHOLD, log_file=LOG_FILE, log_level=LOG_LEVEL) # Worker database monitordb = MonitorDatabase(db_file=DB_FILE, log_file=LOG_FILE, log_level=LOG_LEVEL) # Client database clientdb = ClientDatabase() # Create the main DSage object dsage_server = DSageServer(jobdb, monitordb, clientdb, log_level=LOG_LEVEL) p = _SSHKeyPortalRoot(portal.Portal(Realm(dsage_server))) # Credentials checker p.portal.registerChecker(PublicKeyCredentialsCheckerDB(clientdb)) # HACK: unsafeTracebacks should eventually be TURNED off client_factory = pb.PBServerFactory(p, unsafeTracebacks=True) # Create the looping call that will output the XML file for Dashboard tsk1 = task.LoopingCall(write_stats, dsage_server, STATS_FILE) tsk1.start(5.0, now=False) # Create the PBServerFactory for workers # Use this for unauthorized workers # dsage_worker = DSageWorkerServer(jobdb, log_level=LOG_LEVEL) # worker_factory = WorkerPBServerFactory(dsage_worker) dsage_server.client_factory = client_factory attempts = 0 err_msg = "Could not find an open port after 50 attempts." NEW_CLIENT_PORT = CLIENT_PORT while True: if attempts > 50: log.err(err_msg) log.err('Last attempted port: %s' % (NEW_CLIENT_PORT)) sys.exit(-1) try: try: s = socket.socket(socket.AF_INET, socket.SOCK_STREAM) s.connect(('', NEW_CLIENT_PORT)) port_used = True except socket.error, msg: port_used = False if not port_used: if SSL: ssl_context = ssl.DefaultOpenSSLContextFactory( SSL_PRIVKEY, SSL_CERT) reactor.listenSSL(NEW_CLIENT_PORT, client_factory, contextFactory = ssl_context) break else: reactor.listenTCP(NEW_CLIENT_PORT, client_factory) break else: raise SystemError('Trying to bind to open port: ' + '%s.' % (NEW_CLIENT_PORT)) except (SystemError, error.CannotListenError): attempts += 1 NEW_CLIENT_PORT += 1 except Exception, msg: print 'Exception: ', msg if SSL: print 'Error starting server with SSL enabled, please ' + \ 'check your configuration' else: print 'Error starting server, please check your configuration' sys.exit() if CLIENT_PORT != NEW_CLIENT_PORT: log.msg(DELIMITER) log.msg("***NOTICE***") log.msg("Changing listening port in server.conf " + "to %s" % (NEW_CLIENT_PORT)) log.msg(DELIMITER) log.msg(DELIMITER) log.msg('DSAGE Server') log.msg('Started with PID: %s' % (os.getpid())) if SSL: log.msg('Using SSL: True') else: log.msg('Using SSL: False') log.msg('Listening on port: %s' % (NEW_CLIENT_PORT)) log.msg(DELIMITER) # Code below can be turned on to do countrefs # from sage.dsage.misc.countrefs import logInThread # logInThread(n=15) # reactor.callWhenRunning(create_manhole) # import pdb; pdb.set_trace() if options.noblock: reactor.run(installSignalHandlers=0) else: reactor.run(installSignalHandlers=1) | 1da5dd6b5fc14813a1db017c90bcdc1a88698673 /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/9890/1da5dd6b5fc14813a1db017c90bcdc1a88698673/dsage_server.py | [
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if caps is not None: filters = caps[0] self.width = filters["width"] self.height = filters["height"] timecode = self.pipeline.query_position(gst.FORMAT_TIME)[0] pixbuf = gtk.gdk.pixbuf_new_from_data(buff.data, gtk.gdk.COLORSPACE_RGB, False, 8, self.width, self.height, self.width * 3) | if caps is None: self.success = False self.disconnect() self.done() return False filters = caps[0] width = filters["width"] height = filters["height"] timecode = self.thumbnail_pipeline.query_position(gst.FORMAT_TIME)[0] pixbuf = gtk.gdk.pixbuf_new_from_data( buff.data, gtk.gdk.COLORSPACE_RGB, False, 8, width, height, width * 3) | def buffer_probe_handler_real(self, pad, buff, name): """Capture buffers as gdk_pixbufs when told to.""" if self.grabit: caps = buff.caps if caps is not None: filters = caps[0] self.width = filters["width"] self.height = filters["height"] timecode = self.pipeline.query_position(gst.FORMAT_TIME)[0] pixbuf = gtk.gdk.pixbuf_new_from_data(buff.data, gtk.gdk.COLORSPACE_RGB, False, 8, self.width, self.height, self.width * 3) pixbuf.save(self.thumbnail_filename, "png") del pixbuf self.success = True self.disconnect() self.done() return False | 9ec3a8ff57978fde4b3a57d656b012c6d994d233 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/12354/9ec3a8ff57978fde4b3a57d656b012c6d994d233/gst_extractor.py | [
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return [ id for d, id in facs ] | return [ id for d, n, id in facs ] | def primes_above(self, x, degree=None): r""" Return prime ideals of self lying over x. INPUT: - ``x``: usually an element or ideal of self. It should be such that self.ideal(x) is sensible. This excludes x=0. - ``degree`` (default: None): None or an integer. If None, find all primes above x of any degree. If an integer, find all primes above x such that the resulting residue field has exactly this degree. OUTPUT: A list of prime ideals of self lying over x. If degree is specified and no such ideal exists, returns the empty list. The output is sorted by residue degree first, then by underlying prime (or equivalently, by norm). EXAMPLES:: sage: x = ZZ['x'].gen() sage: F.<t> = NumberField(x^3 - 2) :: sage: P2s = F.primes_above(2) sage: P2s # random [Fractional ideal (-t)] sage: all(2 in P2 for P2 in P2s) True sage: all(P2.is_prime() for P2 in P2s) True sage: [ P2.norm() for P2 in P2s ] [2] :: sage: P3s = F.primes_above(3) sage: P3s # random [Fractional ideal (t + 1)] sage: all(3 in P3 for P3 in P3s) True sage: all(P3.is_prime() for P3 in P3s) True sage: [ P3.norm() for P3 in P3s ] [3] The ideal (3) is totally ramified in F, so there is no degree 2 prime above 3:: sage: F.primes_above(3, degree=2) [] sage: [ id.residue_class_degree() for id, _ in F.ideal(3).factor() ] [1] Asking for a specific degree works:: sage: P5_1s = F.primes_above(5, degree=1) sage: P5_1s # random [Fractional ideal (-t^2 - 1)] sage: P5_1 = P5_1s[0]; P5_1.residue_class_degree() 1 :: sage: P5_2s = F.primes_above(5, degree=2) sage: P5_2s # random [Fractional ideal (t^2 - 2*t - 1)] sage: P5_2 = P5_2s[0]; P5_2.residue_class_degree() 2 | b1ff2cfec2ee360f7df9341f799c02aaa308934c /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/9890/b1ff2cfec2ee360f7df9341f799c02aaa308934c/number_field.py | [
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u"""returns 0 if no cookie configured, 1 if cookie configured, 2 if cookie already configured (even if it is for a null value)""" | u"""returns 0 if no cookie configured, 1 if cookie configured, 2 if cookie already configured (even if it is for a null value)""" | def cookieHandler(): u"""returns 0 if no cookie configured, 1 if cookie configured, 2 if cookie already configured (even if it is for a null value)""" global cj returnValue = 2 logStatusMsg(u"""testing cookieFile settings""", 5) if cj == 1: pass elif cj == None and not getConfig()['global']['cookieFile']: logStatusMsg(u"""no cookies set""", 5) returnValue = 0 elif getConfig()['global']['urllib'] and not isinstance(cj, (cookielib.MozillaCookieJar, cookielib.LWPCookieJar) ): logStatusMsg(u"""attempting to load cookie type: %s """ % getConfig()['global']['cookieType'], 5) cj = cookielib.__getattribute__( getConfig()['global']['cookieType'] )() try: cj.load(getConfig()['global']['cookieFile']) returnValue = 1 logStatusMsg(u"""cookies loaded""", 5) except (cookielib.LoadError, IOError), m: logStatusMsg( unicodeC(m) + u' disabling cookies. To re-enable cookies, stop RSSDler, correct the problem, and restart.', 1) returnValue = 0 elif not getConfig()['global']['urllib'] and not isinstance(cj, (mechanize.MozillaCookieJar, mechanize.LWPCookieJar, mechanize.MSIECookieJar) ): logStatusMsg(u"""attempting to load cookie type: %s """ % getConfig()['global']['cookieType'], 5) cj = mechanize.__getattribute__( getConfig()['global']['cookieType'] )() try: cj.load(getConfig()['global']['cookieFile']) returnValue = 1 logStatusMsg(u"""cookies loaded""", 5) except (mechanize._clientcookie.LoadError, IOError), m: logStatusMsg( unicodeC(m) + u' disabling cookies. To re-enable cookies, stop RSSDler, correct the problem, and restart.', 1) returnValue = 0 return returnValue | 633e00b171a777d923e4aead2f2717108d53a3b9 /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/1664/633e00b171a777d923e4aead2f2717108d53a3b9/rssdler.py | [
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while key == IHEOL: | while key == "IHEOL": | def getcourse(isprobe, akey): "Get a course and distance from the user." key = 0 dquad = copy.copy(game.quadrant) navmode = "unspecified" itemp = "curt" dsect = coord() iprompt = False if game.landed and not isprobe: prout(_("Dummy! You can't leave standard orbit until you")) proutn(_("are back aboard the ship.")) scanner.chew() return False while navmode == "unspecified": if damaged(DNAVSYS): if isprobe: prout(_("Computer damaged; manual navigation only")) else: prout(_("Computer damaged; manual movement only")) scanner.chew() navmode = "manual" key = IHEOL break if isprobe and akey != -1: # For probe launch, use pre-scanned value first time key = akey akey = -1 else: key = scanner.next() if key == IHEOL: proutn(_("Manual or automatic- ")) iprompt = True scanner.chew() elif key == IHALPHA: if scanner.sees("manual"): navmode = "manual" key = scanner.next() break elif scanner.sees("automatic"): navmode = "automatic" key = scanner.next() break else: huh() scanner.chew() return False else: # numeric if isprobe: prout(_("(Manual navigation assumed.)")) else: prout(_("(Manual movement assumed.)")) navmode = "manual" break if navmode == "automatic": while key == IHEOL: if isprobe: proutn(_("Target quadrant or quadrant§or- ")) else: proutn(_("Destination sector or quadrant§or- ")) scanner.chew() iprompt = True key = scanner.next() if key != IHREAL: huh() return False xi = int(round(scanner.real))-1 key = scanner.next() if key != IHREAL: huh() return False xj = int(round(scanner.real))-1 key = scanner.next() if key == IHREAL: # both quadrant and sector specified xk = int(round(scanner.real))-1 key = scanner.next() if key != IHREAL: huh() return False xl = int(round(scanner.real))-1 dquad.i = xi dquad.j = xj dsect.i = xk dsect.j = xl else: # only one pair of numbers was specified if isprobe: # only quadrant specified -- go to center of dest quad dquad.i = xi dquad.j = xj dsect.j = dsect.i = 4 # preserves 1-origin behavior else: # only sector specified dsect.i = xi dsect.j = xj itemp = "normal" if not VALID_QUADRANT(dquad.i,dquad.j) or not VALID_SECTOR(dsect.i,dsect.j): huh() return False skip(1) if not isprobe: if itemp > "curt": if iprompt: prout(_("Helmsman Sulu- \"Course locked in for Sector %s.\"") % dsect) else: prout(_("Ensign Chekov- \"Course laid in, Captain.\"")) # the actual deltas get computed here delta = coord() delta.i = dquad.j-game.quadrant.j + 0.1*(dsect.j-game.sector.j) delta.j = game.quadrant.i-dquad.i + 0.1*(game.sector.i-dsect.i) else: # manual while key == IHEOL: proutn(_("X and Y displacements- ")) scanner.chew() iprompt = True key = scanner.next() itemp = "verbose" if key != IHREAL: huh() return False delta.j = scanner.real key = scanner.next() if key != IHREAL: huh() return False delta.i = scanner.real # Check for zero movement if delta.i == 0 and delta.j == 0: scanner.chew() return False if itemp == "verbose" and not isprobe: skip(1) prout(_("Helmsman Sulu- \"Aye, Sir.\"")) # Course actually laid in. game.dist = delta.distance() game.direc = delta.bearing() if game.direc < 0.0: game.direc += 12.0 scanner.chew() return True | af15867a294e48006eba4fd9997cae401ccbfb05 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/3176/af15867a294e48006eba4fd9997cae401ccbfb05/sst.py | [
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def _load_Files(self): href = os.path.join( self.Get("config_dir", "config") | self.configParser = self._load_Files("files") def _load_Files(self, section): "Load the config file and add it to configParser" href = os.path.join( self.Get("config_dir"), "config") | def _load_Files(self): href = os.path.join( self.Get("config_dir", "config") self.configParser = ConfigParser.ConfigParser() if len( self.configParser.read(href)) == 0: print "No conf file find" for (key, values) in defaultConf.items("): if not key in self.configParser.options(): self.configParser.set("default", key, value) | 7b19abf7d5a6a776a423f65290cc0d136b8b699d /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/11741/7b19abf7d5a6a776a423f65290cc0d136b8b699d/config.py | [
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self._logger.info("Creating tag.") | def _onTag(self, e): try: self._logger.info("Creating tag.") tagID = e.GetId() if self._tagMenu.IsChecked(tagID) == True: # since clicking checks self.setTag(self._track, tagID) else: self.unsetTag(self._track, tagID) self.refreshSelectedTrack() except AttributeError as err: if str(err) != "'MainWindow' object has no attribute '_track'": raise err self._logger.error("No track selected.") return | 6ece34958d0ec2d8d79071a73ea889b1b54b62d3 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/8545/6ece34958d0ec2d8d79071a73ea889b1b54b62d3/GUI.py | [
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"""This is handler dumps the content of POST request to a disk file into the data_dir/dump. Sub-directories are not supported.""" | """This is handler dumps the content of POST/PUT request to a disk file into the data_dir/dump. Sub-directories are not supported.""" | def WriteFile(self): """This is handler dumps the content of POST request to a disk file into the data_dir/dump. Sub-directories are not supported.""" | 762d2db5d5e1b0d7852ddb2efef982b00e897322 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/9392/762d2db5d5e1b0d7852ddb2efef982b00e897322/testserver.py | [
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self.satList.sort(key = lambda x: x[0]) | self.satList.sort(key = self.sortFunc) | def readTransponders(self): # read initial networks from file. we only read files which we are interested in, # which means only these where a compatible tuner exists. self.satellites = { } self.transponders = { } self.transponderscable = { } self.transpondersterrestrial = { } db = eDVBDB.getInstance() if self.hasNimType("DVB-S"): print "Reading satellites.xml" db.readSatellites(self.satList, self.satellites, self.transponders) self.satList.sort(key = lambda x: x[0]) # sort by orbpos #print "SATLIST", self.satList #print "SATS", self.satellites #print "TRANSPONDERS", self.transponders | 406b024501ad0bf0473d08b345de5e94c370804b /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/6652/406b024501ad0bf0473d08b345de5e94c370804b/NimManager.py | [
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if bits[2] != 'for': | if bits[2] != 'in': | def do_tagged_objects(parser, token): """ Retrieves a list of objects for a given Model which are tagged with a given Tag and stores them in a context variable. The tag must be an instance of a ``Tag``, not the name of a tag. The model is specified in ``[appname].[modelname]`` format. Example usage:: {% tagged_objects foo_tag in tv.Model as object_list %} """ bits = token.contents.split() if len(bits) != 6: raise TemplateSyntaxError('%s tag requires exactly five arguments' % bits[0]) if bits[2] != 'for': raise TemplateSyntaxError("second argument to %s tag must be 'in'" % bits[0]) if bits[4] != 'as': raise TemplateSyntaxError("fourth argument to %s tag must be 'as'" % bits[0]) return TaggedObjectsNode(bits[1], bits[3], bits[5]) | 95ef388684f261e416d45f7a2ad1caf18331dcb2 /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/4290/95ef388684f261e416d45f7a2ad1caf18331dcb2/tagging_tags.py | [
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""").replace('\n', os.linesep) | """) | def testBufferOutputAddErrorOrFailure(self): for message_attr, add_attr, include_error in [ ('errors', 'addError', True), ('failures', 'addFailure', False), ('errors', 'addError', True), ('failures', 'addFailure', False) ]: result = self.getStartedResult() buffered_out = sys.stdout buffered_err = sys.stderr result._original_stdout = StringIO() result._original_stderr = StringIO() | 93232660bb96b8ab10de393850007b49b0cc595c /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/8546/93232660bb96b8ab10de393850007b49b0cc595c/test_result.py | [
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Invenio (formerly CDSWare), then you should not proceed with | Invenio (formerly CDSware), then you should not proceed with | def tmpl_admin_migrate_formats(self, ln): """ Basic page to warn user that migration of formats to format templates is not straightforward """ _ = gettext_set_language(ln) # load the right message language out = '''<p>The migration of format is not completely staightforward. Here are some advice for the migration:</p> <ol> <li>If you do not have modified original formats provided by default in CDS Invenio (formerly CDSWare), then you should not proceed with this step.</li> <li>If you have only made small changes to the original formats provided by default in CDS Invenio (formerly CDSWare), then you should not proceed with this step, but compare your modified files with the new provided files and make changes manually.</li> <li>If you have created totally new formats or made large modifications to the provided one, we still advice you not to use this tool and make changes by yourself. However, you can try to run this translation tool as a starting point. If you have made HTML prototypes of the formats, then you would better start from the prototypes.</li> </ol> <p>In any case you should fill the table that maps text labels to a Marc codes BEFORE doing this migration, which should help you to write new formats (and also help you manage fields of the system).<br/> Here are some explanations that can help you understand why we advice you to rewrite format manually:</p> <p>The new BibFormat now uses format files that separate the presentation from the business logic, which is something that cannot be completely automated. The formats will be moved to new kinds of configuration files, called "<i>Format templates</i> (for the presentation) and "<i>Format elements</i> (for the part that binds the record in database to the format template). Format templates are written in HTML. Format elements are written in Python. However basic format elements do not even need to be written, as BibFormat can guess which field of a record it has to retrieve by looking at an internal mapping table (maps a label to a marc code). It is why it is important that you fill this table correctly BEFORE running the translation of the formats. </p> <p>This migration tool will do as much as possible to translate your formats in these new kind of files. It will create format templates files corresponding to your formats, and will include an attempt of translation + the original code as comment. Empty format elements files will be created whenever necessary.</p>''' | 505c3d30a955c667b9991b574b161cdc797b0161 /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/2763/505c3d30a955c667b9991b574b161cdc797b0161/bibformat_migration_kit_templates.py | [
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p1, p2 = self.o.mousepoints(event) v2 = norm(p2-p1) px = ptonline(a.posn(), p1, v2) | px = self.dragto(a.posn(), event) | def leftShiftDrag(self, event): """ drag the new atom around | c3b33ebb3c32b24b8ca0870be88dba2058d5d0b6 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/11221/c3b33ebb3c32b24b8ca0870be88dba2058d5d0b6/depositMode.py | [
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self.x[i].t = val | self.x[i].t = (c_uint * (len(val) + 1))() self.x[i].t[0] = len(val) for j, num in enumerate(val): self.x[i].t[j+1] = num | def __init__(self, stringSVM, labels, values): | 50217656cb09ddf6382337cca40b8f4397b91010 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/14420/50217656cb09ddf6382337cca40b8f4397b91010/StringSVM.py | [
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candidates) | addresses) | def locate_many(self, domain, role=None, maxservers=None): """Locate a list of up to `maxservers' of domain controllers.""" if role is None: role = 'dc' if maxservers is None: maxservers = self._maxservers if role not in ('dc', 'gc', 'pdc'): raise ValueError, 'Role should be one of "dc", "gc" or "pdc".' if role == 'pdc': maxservers = 1 domain = domain.upper() self.m_logger.debug('locating domain controllers for %s (role %s)' % (domain, role)) key = (domain, role) if key in self.m_cache: stamp, nrequested, servers = self.m_cache[key] now = time.time() if now - stamp < self._timeout and nrequested >= maxservers: self.m_logger.debug('domain controllers found in cache') return servers self.m_logger.debug('domain controllers not in cache, going to network') servers = [] candidates = [] if self.m_site is None and not self.m_site_detected: self.m_site = self._detect_site(domain) self.m_site_detected = True if self.m_site and role != 'pdc': query = '_ldap._tcp.%s._sites.%s._msdcs.%s' % \ (self.m_site, role, domain.lower()) answer = self._dns_query(query, 'SRV') candidates += self._order_dns_srv(answer) query = '_ldap._tcp.%s._msdcs.%s' % (role, domain.lower()) answer = self._dns_query(query, 'SRV') candidates += self._order_dns_srv(answer) candidates = self._extract_addresses_from_srv(candidates) self._remove_duplicates(candidates) replies = [] netlogon = NetlogonClient() for i in range(0, len(candidates), maxservers): for addr in candidates[i:i+maxservers]: addr = (addr, LDAP_PORT) netlogon.query(addr, domain) replies += netlogon.call() if self._sufficient_domain_controllers(replies, role, maxservers): break result = self._select_domain_controllers(replies, role, maxservers, candidates) servers = self._extract_addresses_from_netlogon(result) self.m_logger.debug('found %d domain controllers' % len(servers)) now = time.time() self.m_cache[key] = (now, maxservers, servers) return servers | e4f0f07a232f0948ef6daae133ae57183267e3a3 /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/11970/e4f0f07a232f0948ef6daae133ae57183267e3a3/locate.py | [
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return isntrList | return instrList | def AddInstruments(self, instrTuples): """ Adds one or more instruments to the Project, and ensures that they are all appended to the undo stack as a single atomic action. Parameters: instrTuples -- a list of tuples containing name and type that will be passed to AddInstrument(). Returns: A list of the added Instruments. """ undoAction = self.NewAtomicUndoAction() instrList = [] for name, type in instrTuples: instr = self.AddInstrument(name, type, _undoAction_=undoAction) instrList.append(instr) return isntrList | 05cec31478852c794ce54bdd1c733e5f77c85d18 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/10033/05cec31478852c794ce54bdd1c733e5f77c85d18/Project.py | [
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print("Materials in groups:",mat) print("Textures in groups:",tex) file.close() | file.close() | def load_msh(filename,orbiterpath,convert_coords): '''Read MSH file''' print("filepath=",filename,"orbiterpath=",orbiterpath) file=open(filename,"r") s=file.readline(); if s!='MSHX1\n': print("This file is not orbiter mesh: ",s) return else: print("Orbiter mesh format detected ") n_groups=0 #N of groups from header n_materials=0 #N of mats from header n_textures=0 #N of texs from header n_grp=0 #real N of groups mat=[] #mats in group (int) tex=[] #texs in group (int) groups=[] #groups description [label(str),mat(int),tex(int),nv(int),nt(int),obj(bpy.data.object)] materials=[] #materials description [name,[diff RGBA],[amb RGBA],[spec RGBAP],[emit RGBA]] textures=[] #[texture filename, texture name] while True: s=file.readline() if s=='': break; v=s.split() #print (v) #------Reading GROUPS section------------- if v[0]=="GROUPS": print("Reading groups:") n_groups=int(v[1]); n_mat=0; n_tex=0 #group material and texture label="" while n_grp<n_groups: s1=file.readline(); v1=s1.split() #if v1[0]=="NONORMAL": # print("NONORMAL!") if v1[0]=="LABEL": label=v1[1] if v1[0]=="MATERIAL": n_mat=int(v1[1]) #1..n if v1[0]=="TEXTURE": n_tex=int(v1[1]) #1..n #Reading geometry if v1[0]=="GEOM": vtx=[] tri=[] norm=[] uv=[] nv=int(v1[1]) nt=int(v1[2]) #print ("Group No:",n_grp," verts=",nv," tris=",nt) for n in range(nv): s2=file.readline(); v2=s2.split(); #print(v2); if convert_coords: vtx.append([-float(v2[0]),-float(v2[2]),float(v2[1])])# convert from left-handed coord system else: vtx.append([float(v2[0]),float(v2[1]),float(v2[2])]) #without conversion if len(v2)>5: #there are normals (not vtx+uvs only) #should I convert the normals? norm.append([float(v2[3]),float(v2[4]),float(v2[5])]) if len(v2)==8: #there are normals and uvs if convert_coords: #in Blender, (0,0) is the upper-left corner. #in Orbiter -- lower-left corner. So I must invert V axis uv.append([float(v2[6]),1.0-float(v2[7])]) else: uv.append([float(v2[6]),float(v2[7])]) elif len(v2)==5: #there are only uvs if convert_coords: uv.append([float(v2[3]),1.0-float(v2[4])]) else: uv.append([float(v2[3]),float(v2[4])]) for n in range(nt): #read triangles s2=file.readline(); v2=s2.split(); if convert_coords: tri.append([int(v2[0]),int(v2[2]),int(v2[1])]) #reverted triangle else: tri.append([int(v2[0]),int(v2[1]),int(v2[2])]) #non reverted triangle #print (vtx) #print(norm) n_grp=n_grp+1; if label=='': label="ORBGroup"+str(n_grp) obj=create_mesh(label,vtx,tri,norm,uv) if n_mat!=0: mat.append(n_mat) if n_tex!=0: tex.append(n_tex) groups.append([label,n_mat,n_tex,nv,nt,obj]) label="" #--------------Reading MATERIALS section----------------------- elif v[0]=="MATERIALS": n_materials=int(v[1]) print("-------Reading Materials section,nmats=",n_materials,"------------") #material names for i in range (n_materials): materials.append([file.readline().strip()]) #material properties for i in range (n_materials): file.readline(); # TODO: name checking for n in range(4): s1=file.readline() v1=s1.split() print("Reading material component,n=",n," comp=",v1) if (n==2)and(len(v1)==5): #Specular,5 components materials[i].append([float(v1[0]),float(v1[1]),float(v1[2]),float(v1[3]),float(v1[4])]) else: #Other, 4 components materials[i].append([float(v1[0]),float(v1[1]),float(v1[2]),float(v1[3])]) #---------------Reading TEXTURES section------------------ elif v[0]=="TEXTURES": n_textures=int(v[1]); for i in range(n_textures): textures.append([file.readline().strip(),"ORBTexture"+str(i)]) print(""); print("==========================Summary===========================================") print("Headers: groups=",n_groups," materials=",n_materials," textures=",n_textures) print("\nData:\nGroups:") print(groups,"\nReal No=",len(groups)) print("Materials:",materials) print("Textures:",textures) print("Materials in groups:",mat) print("Textures in groups:",tex) #file file.close() create_materials(groups,materials,textures,orbiterpath) return{"FINISHED"} | a742957b6ee3c17a1d5ddaf38dbe115cb0e00154 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/10993/a742957b6ee3c17a1d5ddaf38dbe115cb0e00154/io_import_msh.py | [
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if debug_prints: print "got a crash but seh is intact, aborting" | logger.log_text("got a crash but seh is intact, aborting") | def exception(self, event): if event.is_first_chance(): event.continueStatus = win32.DBG_EXCEPTION_NOT_HANDLED if self.testing: if self.checkSnapshotPage(event): if debug_prints: print "updated snapshot" event.continueStatus = win32.DBG_CONTINUE elif hasattr(event, 'get_fault_type') and event.get_fault_type() == win32.EXCEPTION_EXECUTE_FAULT: # XXX FIXME # if the crash is a DEP fault I get stuck here # forever and no SEH is used at all! # more research is needed to see if it's indeed a # protection of the OS or a bug in my debugger :/ if debug_prints: print "dep fault, aborting" self.process.kill() | 6d6079c7bcc0ba519b666a5d46e251aede9525d0 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/7261/6d6079c7bcc0ba519b666a5d46e251aede9525d0/sehtest.py | [
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treebuilder = treebuilders.simpletree | treebuilder = treebuilders.simpletree.TreeBuilder | def parse(): optParser = getOptParser() opts,args = optParser.parse_args() try: f = args[-1] except IndexError: print "No filename provided. Use -h for help" sys.exit(1) if opts.treebuilder is not None: try: #This isn't a great way to do this exec("import treebuilders.%s")%opts.treebuilder.split(".")[0] treebuilder = eval("treebuilders.%s"%opts.treebuilder) except NameError: print "Treebuilder %s not found"%opts.treebuilder raise except: treebuilder = treebuilders.simpletree.TreeBuilder else: import treebuilders.simpletree treebuilder = treebuilders.simpletree p = parser.HTMLParser(tree=treebuilder) if opts.profile: import hotshot import hotshot.stats prof = hotshot.Profile('stats.prof') prof.runcall(p.parse, f, False) prof.close() # XXX - We should use a temp file here stats = hotshot.stats.load('stats.prof') stats.strip_dirs() stats.sort_stats('time') stats.print_stats() elif opts.time: import time t0 = time.time() document = p.parse(f) t1 = time.time() print p.tree.testSerializer(document) if opts.error: print "\nParse errors:\n" + "\n".join(p.errors) t2 = time.time() print "\n\nRun took: %fs (plus %fs to print the output)"%(t1-t0, t2-t1) else: document = p.parse(f) print document print p.tree.testSerializer(document) if opts.error: print "\nParse errors:\n" + "\n".join(p.errors) | b99fff6c5e538187360d1c1bec19f4147addb1ed /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/4487/b99fff6c5e538187360d1c1bec19f4147addb1ed/parse.py | [
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def __init__(self, allow_none): | def __init__(self, allow_none, encoding): | def __init__(self, allow_none): self.funcs = {} self.instance = None self.allow_none = allow_none | 2234f2d789905def1599dba588da16bbe4b99357 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/3187/2234f2d789905def1599dba588da16bbe4b99357/SimpleXMLRPCServer.py | [
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assert not filter(lambda x: isinstance(x,LCActionFlowable),V),'LCActionFlowables not allowed in sublists' | assert not [x for x in V if isinstance(x,LCActionFlowable)],'LCActionFlowables not allowed in sublists' | def _flowableSublist(V): "if it isn't a list or tuple, wrap it in a list" if type(V) not in (ListType, TupleType): V = V is not None and [V] or [] from doctemplate import LCActionFlowable assert not filter(lambda x: isinstance(x,LCActionFlowable),V),'LCActionFlowables not allowed in sublists' return V | af20f9e0bc90c57f1430ca9650389ab64c8ea9f1 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/3878/af20f9e0bc90c57f1430ca9650389ab64c8ea9f1/flowables.py | [
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s.quit() if debug: smtplib.stderr = oldstderr | try: s.quit() if debug: smtplib.stderr = oldstderr except: pass | def _email_send(message, openobject_id=None, debug=False): """Low-level method to send directly a Message through the configured smtp server. :param message: an email.message.Message to send :param debug: True if messages should be output to stderr before being sent, and smtplib.SMTP put into debug mode. :return: True if the mail was delivered successfully to the smtp, else False (+ exception logged) """ if openobject_id: message['Message-Id'] = "<%s-openobject-%s@%s>" % (time.time(), openobject_id, socket.gethostname()) try: oldstderr = smtplib.stderr s = smtplib.SMTP() try: # in case of debug, the messages are printed to stderr. if debug: smtplib.stderr = WriteToLogger() s.set_debuglevel(int(bool(debug))) # 0 or 1 s.connect(smtp_server, config['smtp_port']) if ssl: s.ehlo() s.starttls() s.ehlo() if config['smtp_user'] or config['smtp_password']: s.login(config['smtp_user'], config['smtp_password']) s.sendmail(email_from, flatten([email_to, email_cc, email_bcc]), message.as_string()) finally: s.quit() if debug: smtplib.stderr = oldstderr except Exception, e: _logger.error('could not deliver email', exc_info=True) return False return True | 478ab1c86d3d35f3b5c2e40276f5574c62d56543 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/7397/478ab1c86d3d35f3b5c2e40276f5574c62d56543/misc.py | [
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cp.set("gip_tests", "enable_glite", "False") | cp.set("gip_tests", "results_dir", results_dir) | def interpolateConfig(cp): if cp_get(cp, "gip_tests", "site_names", "") == "": cp.set("gip_tests", "site_names", cp_get(cp, "site", "name", "")) if cp_get(cp, "gip_tests", "site_dns", "") == "": host_parts = cp_get(cp, "ce", "name", "").split('.') site_dns = "%s.%s" % (host_parts[:-2], host_parts[:-1]) cp.set("gip_tests", "site_dns", site_dns) if cp_get(cp, "gip_tests", "required_site", "") == "": cp.set("gip_tests", "required_sites", cp_get(cp, "gip_tests", "site_names", "")) grid = cp_get(cp, "site", "group", "") cp.set("gip_tests", "bdii_port", "2170") cp.set("gip_tests", "egee_port", "2170") cp.set("gip_tests", "interop_url", "http://oim.grid.iu.edu/publisher/get_osg_interop_bdii_ldap_list.php?grid=%s&format=html" % grid) if "ITB" in grid: cp.set("bdii", "endpoint", "ldap://is-itb.grid.iu.edu:2170") cp.set("gip_tests", "bdii_addr", "is-itb.grid.iu.edu") cp.set("gip_tests", "egee_bdii", "pps-bdii.cern.ch") cp.set("gip_tests", "egee_bdii_conf_url", "http://egee-pre-production-service.web.cern.ch/egee-pre-production-service/bdii/pps-all-sites.conf") web_server = "http://is-itb.grid.iu.edu" else: cp.set("gip_tests", "bdii_addr", "is.grid.iu.edu") cp.set("gip_tests", "egee_bdii", "lcg-bdii.cern.ch") cp.set("gip_tests", "egee_bdii_conf_url", "http://lcg-bdii-conf.cern.ch/bdii-conf/bdii.conf") web_server = "http://is.grid.iu.edu" cp.set("gip_tests", "update_url", web_server + "/cgi-bin/status.cgi") cp.set("gip_tests", "schema_check_url", web_server + "/data/cemon_processed_osg/%s.processed?which=%s") cp.set("gip_tests", "validator_url", web_server + "/data/cemon_processed_osg/%s.processed?which=%s") if cp_get(cp, "gip_tests", "compare_excludes", "") == "": compare_excludes="GlueCEStateFreeJobSlots,GlueCEStateRunningJobs,GlueCEStateTotalJobs,GlueSiteLocation,GlueSAStateAvailableSpace,GlueSAStateUsedSpace" cp.set("gip_tests", "compare_excludes", compare_excludes) if cp_get(cp, "gip_tests", "enable_glite", "") == "": cp.set("gip_tests", "enable_glite", "False") if cp_get(cp, "gip_tests", "results_dir", "") == "": results_dir = os.path.expandvars("$VDT_LOCATION/apache/htdocs/") cp.set("gip_tests", "enable_glite", "False") | bef31ea77737a7f712e6154212174ef981e1beea /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/12088/bef31ea77737a7f712e6154212174ef981e1beea/gip_testing.py | [
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if cellNr >= self.programChain.cellCount: | if (self.cell.blockMode == \ dvdread.CELL_BLOCK_MODE_ANGLE_FIRST or \ self.cell.blockMode == \ dvdread.CELL_BLOCK_MODE_ANGLE_MIDDLE): cellNr += 1 nextMode = self.programChain.getCell(cellNr).blockMode while nextMode != dvdread.CELL_BLOCK_MODE_ANGLE_LAST: cellNr += 1 nextMode = self.programChain.getCell(cellNr).blockMode cellNr += 1 if cellNr > self.programChain.cellCount: | def linkCell(self, cellNr, sectorNr=None): """Link to the specified cell. | c517613690cb665282fcaf9ca4252741af236776 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/5222/c517613690cb665282fcaf9ca4252741af236776/machine.py | [
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boolOptionsGlobal = ['runOnce', 'active', 'rssFeed', 'urllib', 'noClobber'] | boolOptionsGlobal = ['runOnce', 'active', 'rssFeed', 'urllib', 'noClobber', 'debug'] | def getSaved( filename=None, unset=False): u"""Return an instance of the SaveProcessor class creating one if needed""" global saved if unset: saved = None elif not saved: saved = SaveProcessor(saveFileName=filename) return saved | cb06f1645b77b7012f9195d9b9e4a000a0842687 /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/1664/cb06f1645b77b7012f9195d9b9e4a000a0842687/rssdler.py | [
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str += '(type=' + epytext.to_html(param.type()) | str += '(type=' + dom_to_html(param.type(), container) | def _func_details(self, functions, cls, heading='Function Details'): """Return a detailed description of the functions in a class or module.""" functions = self._sort(functions) if len(functions) == 0: return '' str = self._table_header(heading, 'details')+'</table>' | b1b93a7c8720ea1ae0c715da86bbf6fe1dbf094a /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/3512/b1b93a7c8720ea1ae0c715da86bbf6fe1dbf094a/html.py | [
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hoftQscanLinks += " <img src=\"" + hoft_qscan[i + len(ifolist) - 1] + "/" + gpstime0 + "_" + ifo + ":" + strain + "_1.00_spectrogram_whitened_thumbnail.png\" width=\"50%\"><br>" hoftQscanLinks += " <img src=\"" + hoft_qscan[i + len(ifolist) - 1] + "/" + gpstime0 + "_" + ifo + ":" + strain + "_16.00_spectrogram_whitened_thumbnail.png\" width=\"50%\"><br>" | hoftQscanLinks += " <img src=\"" + hoft_qscan[i + len(ifolist) - 1] + "/" + gpstime0 + "_" + ifo + ":" + strain + "_1.00_spectrogram_whitened.thumb.png\" width=\"50%\"><br>" hoftQscanLinks += " <img src=\"" + hoft_qscan[i + len(ifolist) - 1] + "/" + gpstime0 + "_" + ifo + ":" + strain + "_16.00_spectrogram_whitened.thumb.png\" width=\"50%\"><br>" | def getFileMatchingTrigger(jobname,string_id,file_list=False): if os.access(jobname,os.F_OK): filesInDir = os.listdir(jobname) fileList = [] for paramFile in filesInDir: if fnmatch.fnmatch(paramFile, "*"+string_id+"*.html"): if file_list: fileList.append("../"+jobname+"/"+paramFile) else: return "../"+jobname+"/"+paramFile if fileList: return fileList else: return False else: return False | 9273b7b0fb17e529b5b4f6f9baeb0fb70e722be9 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/3592/9273b7b0fb17e529b5b4f6f9baeb0fb70e722be9/makeCheckList.py | [
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the sorted list of unique numbers described by the ranges. | the sorted list of unique numbers described by the ranges. A range with a positive step describes the offsets (first + n * step) where n is an integer such that first <= offset <= last. A range with a negative step describes the offsets (first + n * step) where n is an integer such that last <= offset <= first. | def parse_slidespec(slidespec): """ Accepts a string in the format instrument=first:last:step[,first:last:step]... and returns the tuple (instrument, [offset1, offset2, ....]) where the offsets are the sorted list of unique numbers described by the ranges. Example: >>> parse_slidespec("H1=-5:+5:0.5") ('H1', [-5.0, -4.5, -4.0, -3.5, -3.0, -2.5, -2.0, -1.5, -1.0, -0.5, 0.0, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0]) """ try: instrument, rangespec = slidespec.split("=") except ValueError: raise ValueError, "cannot parse time slide \"%s\"" % slidespec offsets = set() for range in rangespec.split(","): try: first, last, step = map(float, range.split(":")) except ValueError: raise ValueError, "malformed range \"%s\" in \"%s\"" % (range, rangespec) if step == 0: if first != last: raise ValueError, "divide by zero in range \"%s\"" % range offsets.add(first) continue if (last - first) / step < 0.0: raise ValueError, "step has wrong sign in range \"%s\"" % range i = 0 while True: x = first + i * step if x > last: break offsets.add(x) i += 1 offsets = list(offsets) offsets.sort() return instrument.strip(), offsets | 3280eb72d42d7add55fe0714f37c98d2e461410d /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/3592/3280eb72d42d7add55fe0714f37c98d2e461410d/ligolw_tisi.py | [
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st t1, seg, [scale, index, t2], disp | st t1, seg, [1, t2, t7], disp | def macroop BTC_P_R { rdip t7 limm t1, imm srai t2, t1, "(env.dataSize == 8) ? 3 : ((env.dataSize == 4) ? 2 : 1)" limm t3, 1 rol t3, t3, reg ldst t1, seg, [1, t2, t7] sext t0, t1, reg, flags=(CF,) xor t1, t1, t3 st t1, seg, [scale, index, t2], disp | 67fee0102648eb597c8c2a368da5f37f4b13b78b /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/6787/67fee0102648eb597c8c2a368da5f37f4b13b78b/bit_test.py | [
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self.sage._expect.expect(self.sage._prompt, timeout=timeout) | e.expect(self.sage._prompt, timeout=timeout) | def stop(self): """ Stops the current worker and resets it's internal state. """ INTERRUPT_TRIES = 20 timeout = 0.3 try: for i in range(INTERRUPT_TRIES): self.sage._expect.sendline('q') self.sage._expect.sendline(chr(3)) # send ctrl-c try: self.sage._expect.expect(self.sage._prompt, timeout=timeout) success = True break except (pexpect.TIMEOUT, pexpect.EOF), msg: if self.log_level > 3: log.err("Trying to interrupt SAGE (try %s)..." % i) except Exception, msg: log.err("[Worker %s] Could not do a soft reset, performing a hard reset now.") if not success: pid = self.__sage.pid() cmd = 'kill -9 -%s'%pid os.system(cmd) self.sage = Sage() self.sage.reset() self.free = True self.job = None | b26ee276ff3afed683baa8910a742216978dfeee /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/9890/b26ee276ff3afed683baa8910a742216978dfeee/dsage_worker.py | [
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A 4 by :math:`$(n-1)$` matrix ``Z`` is returned. At the :math:`$i$`th iteration, clusters with indices ``Z[i, 0]`` and ``Z[i, 1]`` are combined to form cluster :math:`$n + i$`. A cluster with an index less than :math:`$n$` corresponds to one of the :math:`$n$` original observations. The distance between | A 4 by :math:`(n-1)` matrix ``Z`` is returned. At the :math:`i`-th iteration, clusters with indices ``Z[i, 0]`` and ``Z[i, 1]`` are combined to form cluster :math:`n + i`. A cluster with an index less than :math:`n` corresponds to one of the :math:`n` original observations. The distance between | def linkage(y, method='single', metric='euclidean'): """ Performs hierarchical/agglomerative clustering on the condensed distance matrix y. y must be a {n \choose 2} sized vector where n is the number of original observations paired in the distance matrix. The behavior of this function is very similar to the MATLAB(TM) linkage function. A 4 by :math:`$(n-1)$` matrix ``Z`` is returned. At the :math:`$i$`th iteration, clusters with indices ``Z[i, 0]`` and ``Z[i, 1]`` are combined to form cluster :math:`$n + i$`. A cluster with an index less than :math:`$n$` corresponds to one of the :math:`$n$` original observations. The distance between clusters ``Z[i, 0]`` and ``Z[i, 1]`` is given by ``Z[i, 2]``. The fourth value ``Z[i, 3]`` represents the number of original observations in the newly formed cluster. The following linkage methods are used to compute the distance :math:`$d(s, t)$` between two clusters :math:`$s$` and :math:`$t$`. The algorithm begins with a forest of clusters that have yet to be used in the hierarchy being formed. When two clusters :math:`$s$` and :math:`$t$` from this forest are combined into a single cluster :math:`$u$`, :math:`$s$` and :math:`$t$` are removed from the forest, and :math:`$u$` is added to the forest. When only one cluster remains in the forest, the algorithm stops, and this cluster becomes the root. A distance matrix is maintained at each iteration. The ``d[i,j]`` entry corresponds to the distance between cluster :math:`$i$` and :math:`$j$` in the original forest. At each iteration, the algorithm must update the distance matrix to reflect the distance of the newly formed cluster u with the remaining clusters in the forest. Suppose there are :math:`$|u|$` original observations :math:`$u[0], \ldots, u[|u|-1]$` in cluster :math:`$u$` and :math:`$|v|$` original objects :math:`$v[0], \ldots, v[|v|-1]$` in cluster :math:`$v$`. Recall :math:`$s$` and :math:`$t$` are combined to form cluster :math:`$u$`. Let :math:`$v$` be any remaining cluster in the forest that is not :math:`$u$`. :Parameters: Q : ndarray A condensed or redundant distance matrix. A condensed distance matrix is a flat array containing the upper triangular of the distance matrix. This is the form that ``pdist`` returns. Alternatively, a collection of :math:`$m$` observation vectors in n dimensions may be passed as a :math:`$m$` by :math:`$n$` array. method : string The linkage algorithm to use. See the ``Linkage Methods`` section below for full descriptions. metric : string The distance metric to use. See the ``distance.pdist`` function for a list of valid distance metrics. Linkage Methods --------------- The following are methods for calculating the distance between the newly formed cluster :math:`$u$` and each :math:`$v$`. * method=``single`` assigns .. math: d(u,v) = \min(dist(u[i],v[j])) for all points :math:`$i$` in cluster :math:`$u$` and :math:`$j$` in cluster :math:`$v$`. This is also known as the Nearest Point Algorithm. * method=``complete`` assigns .. math: d(u, v) = \max(dist(u[i],v[j])) for all points :math:`$i$` in cluster u and :math:`$j$` in cluster :math:`$v$`. This is also known by the Farthest Point Algorithm or Voor Hees Algorithm. * method=``average`` assigns .. math: d(u,v) = \sum_{ij} \frac{d(u[i], v[j])} {(|u|*|v|) for all points :math:`$i$` and :math:`$j$` where :math:`$|u|$` and :math:`$|v|$` are the cardinalities of clusters :math:`$u$` and :math:`$v$`, respectively. This is also called the UPGMA algorithm. This is called UPGMA. * method='weighted' assigns .. math: d(u,v) = (dist(s,v) + dist(t,v))/2 where cluster u was formed with cluster s and t and v is a remaining cluster in the forest. (also called WPGMA) * method='centroid' assigns .. math: dist(s,t) = euclid(c_s, c_t) where :math:`$c_s$` and :math:`$c_t$` are the centroids of clusters :math:`$s$` and :math:`$t$`, respectively. When two clusters :math:`$s$` and :math:`$t$` are combined into a new cluster :math:`$u$`, the new centroid is computed over all the original objects in clusters :math:`$s$` and :math:`$t$`. The distance then becomes the Euclidean distance between the centroid of :math:`$u$` and the centroid of a remaining cluster :math:`$v$` in the forest. This is also known as the UPGMC algorithm. * method='median' assigns math:`$d(s,t)$` like the ``centroid`` method. When two clusters s and t are combined into a new cluster :math:`$u$`, the average of centroids s and t give the new centroid :math:`$u$`. This is also known as the WPGMC algorithm. * method='ward' uses the Ward variance minimization algorithm. The new entry :math:`$d(u,v)$` is computed as follows, .. math: d(u,v) = \sqrt{\frac{|v|+|s|} {T}d(v,s)^2 + \frac{|v|+|t|} {T}d(v,t)^2 + \frac{|v|} {T}d(s,t)^2} where :math:`$u$` is the newly joined cluster consisting of clusters :math:`$s$` and :math:`$t$`, :math:`$v$` is an unused cluster in the forest, :math:`$T=|v|+|s|+|t|$`, and :math:`$|*|$` is the cardinality of its argument. This is also known as the incremental algorithm. Warning ------- When the minimum distance pair in the forest is chosen, there may be two or more pairs with the same minimum distance. This implementation may chose a different minimum than the MATLAB(TM) version. """ if not isinstance(method, str): raise TypeError("Argument 'method' must be a string.") y = _convert_to_double(np.asarray(y, order='c')) s = y.shape if len(s) == 1: distance.is_valid_y(y, throw=True, name='y') d = distance.num_obs_y(y) if method not in _cpy_non_euclid_methods.keys(): raise ValueError("Valid methods when the raw observations are omitted are 'single', 'complete', 'weighted', and 'average'.") # Since the C code does not support striding using strides. [y] = _copy_arrays_if_base_present([y]) Z = np.zeros((d - 1, 4)) _hierarchy_wrap.linkage_wrap(y, Z, int(d), \ int(_cpy_non_euclid_methods[method])) elif len(s) == 2: X = y n = s[0] m = s[1] if method not in _cpy_linkage_methods: raise ValueError('Invalid method: %s' % method) if method in _cpy_non_euclid_methods.keys(): dm = distance.pdist(X, metric) Z = np.zeros((n - 1, 4)) _hierarchy_wrap.linkage_wrap(dm, Z, n, \ int(_cpy_non_euclid_methods[method])) elif method in _cpy_euclid_methods.keys(): if metric != 'euclidean': raise ValueError('Method %s requires the distance metric to be euclidean' % s) dm = distance.pdist(X, metric) Z = np.zeros((n - 1, 4)) _hierarchy_wrap.linkage_euclid_wrap(dm, Z, X, m, n, int(_cpy_euclid_methods[method])) return Z | 8172e9e1737f1f6d84d1b06fa46e587e764a1a0f /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/5882/8172e9e1737f1f6d84d1b06fa46e587e764a1a0f/hierarchy.py | [
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return self._getCachedInfo()['venue']['name'] | return self._getCachedInfo('venue', 'name') | def getVenueName(self): """Returns the name of the venue where the event is held. """ return self._getCachedInfo()['venue']['name'] | ec1304614ea5bc838c2f5bb83444fc59ac9c26d8 /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/9926/ec1304614ea5bc838c2f5bb83444fc59ac9c26d8/pylast.py | [
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expect(f.read(1), 'z') | expect(f.read(1), b'z') | def expect(got_this, expect_this): if test_support.verbose: print('%r =?= %r ...' % (got_this, expect_this), end=' ') if got_this != expect_this: if test_support.verbose: print('no') raise test_support.TestFailed, 'got %r, but expected %r' %\ (got_this, expect_this) else: if test_support.verbose: print('yes') | f55d86abe0e358709c72f404db4b832ea362c7d9 /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/12029/f55d86abe0e358709c72f404db4b832ea362c7d9/test_largefile.py | [
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builder.getObject(state, name).source = '\n'.join(text).lstrip('\n\t/ ')+'\n/' | obj = builder.getObject(state, name) if obj: obj.source = '\n'.join(text).lstrip('\n\t/ ')+'\n/' | def customQuery(cursor, state, builder): cursor.execute(""" SELECT name, DECODE(line, 1, '/'||chr(10)||'CREATE OR REPLACE ', '')||text FROM user_source WHERE type IN ('%s') ORDER BY name, type, line""" % "', '".join(builder.DbType)) | bfd136ac9ae145198693c941adea2547c628575f /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/760/bfd136ac9ae145198693c941adea2547c628575f/code.py | [
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reg.register_linear_resample(image['data'], remaped_image['data'], M_inverse, imdata['step']) | reg.register_linear_resample(image, remaped_image, M_inverse, step) | def remap_image(image, parm_vector, resample='linear'): """ remaped_image = remap_image(image, parm_vector, resample='linear') rotates and translates image using the 3 angles and 3 translations in the 6-dim parm_vector. The mapping is stored in the 4x4 M_inverse matrix from the get_inverse_mapping method. Parameters ---------- image : {dictionary} image is the source image to be remapped. it is a dictionary with the data as an ndarray in the ['data'] component. parm_vector : {ndarray} parm_vector is the 6-dimensional vector (3 angles, 3 translations) generated from the registration. resample : {'linear', 'cubic'}, optional Returns ------- remaped_image : {dictionary} Examples -------- image = fmri_series[i] x[0:6] = measures[i]['align_rotate'][0:6] # overwrite the fMRI volume with the aligned volume fmri_series[i] = remap_image(image, x, resample='cubic') """ # # remap imageG to coordinates of imageF (creates imageG') # use the 6 dim parm_vector (3 angles, 3 translations) to remap # M_inverse = get_inverse_mappings(parm_vector) (layers, rows, cols) = image['data'].shape # allocate the zero image remaped_image = np.zeros(layers*rows*cols, dtype=np.uint8).reshape(layers, rows, cols) remaped_image = {'data' : remaped_image, 'mat' : image['mat'], 'dim' : image['dim'], 'fwhm' : image['fwhm']} imdata = build_structs() if resample == 'linear': # trilinear interpolation mapping. reg.register_linear_resample(image['data'], remaped_image['data'], M_inverse, imdata['step']) elif resample == 'cubic': # tricubic convolve interpolation mapping. reg.register_cubic_resample(image['data'], remaped_image['data'], M_inverse, imdata['step']) return remaped_image | a0a06507bdbd3322039b726463a7cc1c63e59774 /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/12971/a0a06507bdbd3322039b726463a7cc1c63e59774/_registration.py | [
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fromdate = datetime.datetime.today() todate = datetime.datetime.today() | fromdate = None todate = None | def to_datetime(datestr): numlist = re.findall('\d+', datestr) if len(numlist) != 3: print >>sys.stderr, '%s not in correct format [DD/MM/YYYY]' % datestr return None else: datelist = [] for num in numlist: datelist.append(string.atoi(num)) return datetime.datetime(datelist[2], datelist[1], datelist[0]) | f55a79144368a66b96fa92a55d8cec444dbad926 /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/5095/f55a79144368a66b96fa92a55d8cec444dbad926/supremecourt.py | [
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return self.is_64bit() and self.is_i686() | return self.is_64bit() and self.is_PentiumIV() | def _is_Nocona(self): return self.is_64bit() and self.is_i686() | 19cc4b93b3dd495fd355d77225d3f97e23f85ffb /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/14925/19cc4b93b3dd495fd355d77225d3f97e23f85ffb/cpuinfo.py | [
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capture_temp=False, assert_no_temp=False): | capture_temp=False, assert_no_temp=False, split_cmd=True): | def __init__(self, base_path=None, template_path=None, environ=None, cwd=None, start_clear=True, ignore_paths=None, ignore_hidden=True, capture_temp=False, assert_no_temp=False): """ Creates an environment. ``base_path`` is used as the current working directory, and generally where changes are looked for. If not given, it will be the directory of the calling script plus ``test-output/``. | 1edb8b5be29dbec631d234d0f7427ff0e8b3b22d /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/8710/1edb8b5be29dbec631d234d0f7427ff0e8b3b22d/__init__.py | [
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class SimpleXMLRPCRequestHandler(GenericXMLRPCRequestHandler, SimpleXMLRPCServer.SimpleXMLRPCRequestHandler): | class SimpleXMLRPCRequestHandler(GenericXMLRPCRequestHandler, SimpleXMLRPCServer.SimpleXMLRPCRequestHandler): | def _dispatch(self, method, params): #print 'TERP-CALL : ',method, params import traceback try: n = self.path.split("/")[-1] s = LocalService(n) m = getattr(s, method) s._service._response = None r = m(*params) res = s._service._response if res != None: r = res return r except Exception, e: tb_s = reduce(lambda x, y: x+y, traceback.format_exception( sys.exc_type, sys.exc_value, sys.exc_traceback)) s = str(e) import tools if tools.config['debug_mode']: import pdb tb = sys.exc_info()[2] pdb.post_mortem(tb) raise xmlrpclib.Fault(s, tb_s) | 07f8f4943d0e6d1b45e76498021f6b5ff8ed63dc /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/7397/07f8f4943d0e6d1b45e76498021f6b5ff8ed63dc/netsvc.py | [
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files = popenx(cmdline, 'b') fi = files[0] fo = files[1] if self.have_popen3: fe = files[2] | files = subprocess.Popen(cmdline, stdin = subprocess.PIPE, stdout = subprocess.PIPE, stderr = subprocess.PIPE ) | def run_cgi(self): """Execute a CGI script.""" path = self.path dir, rest = self.cgi_info | 3a145a18c863f2b573b47126f7d6ed35bc3d48af /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/8546/3a145a18c863f2b573b47126f7d6ed35bc3d48af/CGIHTTPServer.py | [
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self.state = (nsdict, ['xml'], []) | self.state = (nsdict, {'xml':''}, {}) | def __init__(self, node, write, **kw): '''Create and run the implementation.''' | 6df2d566784161a533c97fa1bd11ec1e27489fcb /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/13054/6df2d566784161a533c97fa1bd11ec1e27489fcb/c14n.py | [
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} | } | def c_code(self, node, nodename, (x, z, gz), (gx,), sub): fail = sub['fail'] ds0, ds1 = self.ds ignore_border = int(self.ignore_border) return """ if (%(x)s->nd != 4 || %(z)s->nd != 4 || %(gz)s->nd != 4) { PyErr_SetString(PyExc_ValueError, "rank error"); %(fail)s; } if ((NULL == %(gx)s) || (CudaNdarray_HOST_DIMS(%(gx)s)[0] != CudaNdarray_HOST_DIMS(%(x)s)[0]) || (CudaNdarray_HOST_DIMS(%(gx)s)[1] != CudaNdarray_HOST_DIMS(%(x)s)[1]) || (CudaNdarray_HOST_DIMS(%(gx)s)[2] != CudaNdarray_HOST_DIMS(%(x)s)[2]) || (CudaNdarray_HOST_DIMS(%(gx)s)[3] != CudaNdarray_HOST_DIMS(%(x)s)[3])) { Py_XDECREF(%(gx)s); %(gx)s = (CudaNdarray*)CudaNdarray_new_null(); if ((NULL == %(gx)s) || CudaNdarray_alloc_contiguous(%(gx)s, 4, CudaNdarray_HOST_DIMS(%(x)s))) { Py_XDECREF(%(gx)s); %(gx)s = NULL; %(fail)s; } } { //TODO: supporting more output columns than threads // make sure we cover every x row when ignore border isset and there's a border present to be ignored int needs_extra_z_col = %(ignore_border)s && (CudaNdarray_HOST_DIMS(%(x)s)[2] %% %(ds0)s); dim3 grid(CudaNdarray_HOST_DIMS(%(z)s)[0],CudaNdarray_HOST_DIMS(%(z)s)[2] + (needs_extra_z_col ? 1 : 0)); dim3 block(CudaNdarray_HOST_DIMS(%(x)s)[3]); kDownsampleMaxGrad_%(nodename)s<%(ds0)s, %(ds1)s> <<<grid, block>>>( CudaNdarray_HOST_DIMS(%(z)s)[0], CudaNdarray_HOST_DIMS(%(z)s)[1], CudaNdarray_HOST_DIMS(%(z)s)[2], CudaNdarray_HOST_DIMS(%(z)s)[3], CudaNdarray_HOST_DIMS(%(x)s)[2], CudaNdarray_HOST_DIMS(%(x)s)[3], CudaNdarray_DEV_DATA(%(x)s), CudaNdarray_HOST_STRIDES(%(x)s)[0], CudaNdarray_HOST_STRIDES(%(x)s)[1], CudaNdarray_HOST_STRIDES(%(x)s)[2], CudaNdarray_HOST_STRIDES(%(x)s)[3], CudaNdarray_DEV_DATA(%(z)s), CudaNdarray_HOST_STRIDES(%(z)s)[0], CudaNdarray_HOST_STRIDES(%(z)s)[1], CudaNdarray_HOST_STRIDES(%(z)s)[2], CudaNdarray_HOST_STRIDES(%(z)s)[3], CudaNdarray_DEV_DATA(%(gz)s), CudaNdarray_HOST_STRIDES(%(gz)s)[0], CudaNdarray_HOST_STRIDES(%(gz)s)[1], CudaNdarray_HOST_STRIDES(%(gz)s)[2], CudaNdarray_HOST_STRIDES(%(gz)s)[3], CudaNdarray_DEV_DATA(%(gx)s)); CNDA_THREAD_SYNC; cudaError_t err = cudaGetLastError(); if( cudaSuccess != err) { PyErr_Format(PyExc_RuntimeError, "Cuda error: %%s: %%s. (grid: %%i x %%i; block: %%i x %%i x %%i)\\n", "kDownsampleMaxGrad_%(nodename)s", cudaGetErrorString(err), grid.x, grid.y, block.x, block.y, block.z); %(fail)s; } } """ % locals() | 98f8608be75b8b81997fa956395f0063b48ea567 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/12438/98f8608be75b8b81997fa956395f0063b48ea567/blas.py | [
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class RuleLine(object): """A rule line is a single "Allow:" (allowance==1) or "Disallow:" (allowance==0) followed by a path.""" | class RuleLine: """A rule line is a single "Allow:" (allowance==True) or "Disallow:" (allowance==False) followed by a path.""" | def __str__(self): ret = "" for entry in self.entries: ret = ret + str(entry) + "\n" return ret | 9f86ae009f1e74ee040c0d6e683bcba6894a674b /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/4845/9f86ae009f1e74ee040c0d6e683bcba6894a674b/robotparser.py | [
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assert(self.debugPrint("setAvatarPhysicsIndicator()")) | assert self.notify.debugStateCall(self) | def setAvatarPhysicsIndicator(self, indicator): """ indicator is a NodePath """ assert(self.debugPrint("setAvatarPhysicsIndicator()")) self.cWallSphereNodePath.show() | abc151a082286523619150b15b5dc30864de5bde /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/7242/abc151a082286523619150b15b5dc30864de5bde/GravityWalker.py | [
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buffer += key if key == '\n': break return buffer | buffer += key if key == '\n': break finally: curses.raw(False) return buffer.encode(getpreferredencoding()) | def readline(self): """I can't think of any reason why anything other than readline would be useful in the context of an interactive interpreter so this is the only one I've done anything with. The others are just there in case someone does something weird to stop it from blowing up.""" | cd3b707f7e1acfdd7180d26c1bb4a6a98ccb3a75 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/6932/cd3b707f7e1acfdd7180d26c1bb4a6a98ccb3a75/cli.py | [
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(S_IFLNK, "l", S_IFREG, "-", S_IFBLK, "b", S_IFDIR, "d", S_IFCHR, "c", S_IFIFO, "p"), (TUREAD, "r"), (TUWRITE, "w"), (TUEXEC, "x", TSUID, "S", TUEXEC|TSUID, "s"), (TGREAD, "r"), (TGWRITE, "w"), (TGEXEC, "x", TSGID, "S", TGEXEC|TSGID, "s"), (TOREAD, "r"), (TOWRITE, "w"), (TOEXEC, "x", TSVTX, "T", TOEXEC|TSVTX, "t")) | ((S_IFLNK, "l"), (S_IFREG, "-"), (S_IFBLK, "b"), (S_IFDIR, "d"), (S_IFCHR, "c"), (S_IFIFO, "p")), ((TUREAD, "r"),), ((TUWRITE, "w"),), ((TUEXEC|TSUID, "s"), (TSUID, "S"), (TUEXEC, "x")), ((TGREAD, "r"),), ((TGWRITE, "w"),), ((TGEXEC|TSGID, "s"), (TSGID, "S"), (TGEXEC, "x")), ((TOREAD, "r"),), ((TOWRITE, "w"),), ((TOEXEC|TSVTX, "t"), (TSVTX, "T"), (TOEXEC, "x")) ) | def copyfileobj(src, dst, length=None): """Copy length bytes from fileobj src to fileobj dst. If length is None, copy the entire content. """ if length == 0: return if length is None: shutil.copyfileobj(src, dst) return BUFSIZE = 16 * 1024 blocks, remainder = divmod(length, BUFSIZE) for b in xrange(blocks): buf = src.read(BUFSIZE) if len(buf) < BUFSIZE: raise IOError, "end of file reached" dst.write(buf) if remainder != 0: buf = src.read(remainder) if len(buf) < remainder: raise IOError, "end of file reached" dst.write(buf) return | 8bc462fcafe9f11094f0185813f95c0f569b112e /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/8546/8bc462fcafe9f11094f0185813f95c0f569b112e/tarfile.py | [
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